The book Zhuangzi was fixed in its shape by Liu Xiang 刘向, an imperial librarian of the Former Han dynasty 前汉 (206 BCE-8 CE). At that time the book Zhuangzi comprised 52 chapters, while the received version, shaped by the Jin period 晋 (265-420) Daoist scholar Guo Xiang 郭象, has only 33 chapters, divided into three parts: 7 "inner chapters" (neipian 内篇), 15 "outer chapters" (waipian 外篇), and 11 "miscellaneous chapters" (zapian 杂篇). The literary language of the Zhuangzi is very excellent and many parts of the book, in thought as well as in language, seem to stem from one single author, at least the Inner Chapters. The Song period 宋 (960-1279) writer and thinker Su Shi 苏轼 was the first who systematically analyzed the probability of Zhuang Zhou’s authorship and came to the conclusion that the chapters Dao Zhi 盗跖, Yufu 渔父, Rangwang 让王 and Yuejian 说剑 were definitely not written by the philosopher Zhuangzi. The Ming period 明 (1368-1644) collector Jiao Hong 焦竑 argued that the Inner Chapters were quite probably written by one person, but the Outer and Miscellaneous Chapters were additions of later times, especially the Han period. The modern scholar Luo Genze 罗根泽 systematically analysed these doubtful parts of the book. He concluded that some parts included anti-Confucian, or probably anarchist or at least libertinist, sentiments of what he calls "leftist Daoists" (zuopai daojia 左派道家), while others were written by "rightist Daoists" (youpai daojia 右派道家) that were accepting the Confucian order of society. These, and the chapters talking of immortals, were creations of the late Warring States or the early Han period, when Confucianism was not yet defined as the official state doctrine. Wang Shumin 王叔岷 (Zhuangzi jiaoshi 庄子校释) says that the division into inner and outer chapters was an arrangement by Guo Xiang, who therewith followed a common use also to be found in other early texts, and therefore challenges the old theory that the Inner Chapters were originals and therefore more trustworthy than the others. Ma Xulun 马叙伦 (Zhuangzi yizheng 庄子义证) also points at the fact that only very few texts include a part of "miscellaneous chapters". The famous historian of philosophy Feng Youlan 冯友兰, followed this argument and doubted whether the Inner Chapters really contained any original thoughts of Zhuangzi.
During the Han period the book Zhuangzi was not yet regarded with high esteem. Only during the Jin period it became one of the "Three Mysterious Books" (sanxuan 三玄), together with the Yijing 易经 and the Laozi. During the Tang period 唐 (618-907) the philosopher Zhuangzi was deified and the book attributed to him was given the official title of Nanhua zhengjing 南华真经 "Perfect classic of the Southern Flower". The most important commentaries are Zhuangzi zhu 庄子注 by Guo Xiang, Zhuangzi shu 庄子疏 by the Tang period author Cheng Xuanying 成玄英, Lu Deming's 陆德明 phonetic commentary Zhuangzi yinyi 庄子音义, Lin Xiyi's 林希逸 commentary Nanhua zhenjing kouyi 南华真经口义 from the Song period, the Ming period scholar Jiao Hong's Zhuangzi yi 庄子翼, and finally the Qing period 清 (1644-1911) commentaries Zhuangzi jishi 庄子集释 by Guo Qingfan 郭庆藩, Wang Xianqian's 王先谦 Zhuangzi jijie 庄子集解, and the modern commentary Zhuangzi buzheng 庄子补正 by Liu Wendian 刘文典. Other early commentaries were written by Sima Biao 司马彪 and Cui Zhuan 崔譔, fragements of which can be found in the collectaneum Jingdian shiwen 经典释文.

The Zhuangzi is also very important for its information on the proponents of other philosophical schools regularly cited. Zhuangzi expresses his philosophical thoughts by anecdotes which makes the book very amusing and readable, besides of the high literary quality. Many parts of the Zhuangzi are reports about strange countries and fabulous beasts like in the pseudo-geography Shanhaijing 山海经, and supernatural powers of immortals, like in later collections of Daoist biographies like the Liexianzhuan 列仙传. Some critics also say that Zhuangzi in some chapters exerted hypnomancy (interpretation of dreams).
The most widespread and important editions of the Zhuangzi are the facsimile of a Song period print in the collectaneum Xu guyishu 续古逸书, the edition in the Daoist Canon Daozang, the Ming period edition in the Liuzi quanshu 六子全书, produced in the Shide Hall 世德堂, the Shizi quanshu 十子全书 edition by the Juwen Hall 聚文堂, and the Qing period prints in the Zishu ershier zhong 子书二十二种 and the Zhuangzi jishi 庄子集释 published by the Sixian Academy 思贤讲舍 in Changsha. The Zhuangzi is also to be found in the collectanea Sibu congkan 四部丛刊, Baizi quanshu 百子全书, Zhuzi jicheng 诸子集成, Sibu beiyao 四部备要 and Siku quanshu 四库全书.

The book Zhuangzi was at all times very attractive because of its metaphorical language. It is an appealing counterpart and completion of the mysterious and obscure statements in the Daodejing. Zhuangzi's high literary standards made it furthermore a favoured reading of the educated class, even the Confucians. In the 3rd century CE, when Confucianism was somewhat discredited by the failure of the state administration, Daoism was en vogue, especially in the syncretist form of the so-called "School of Mysteries" (xuanxue 玄学) that combined Confucian ideas with that of the anti-state attitude of Laozi and Zhuangzi. All early commentators to the Zhuangzi, like Xiang Xiu or Guo Xiang, were representants of the School of Mysteries. In the next centuries the Buddhist concept of prajñā (Chinese transliteration bōrě 般若, sic!), the universal wisdom that penetrates all objects in the universe, was merged with Zhuangzi's understanding of the Dao. Other aspects of Daoism were also to be found in Buddhist religion, like samādhi "mediation", which can be compared with Zhuangzi's "sitting and forgetting". The monk Zhidun 支遁 compiled an essay to Zhuangzi's chapter Xiaoyaoyou, and it is known that the monk Huiyuan 慧远 in his early years studied the Confucian Classics as well as Laozi and Zhuangzi. Finally, Zhuangzi's description of the Dao laid the foundation for the Neo-Confucian interpretation of the universal or Heavenly order (tianli 天理), which was not only in principle the same as the Daoist "Way", but also implanted the positive character of the Confucian order of society into the hearts of all humans.