Objective] Explain the intentions of those famous TCM combinations for disease according to Shennong Bencao Jing. [Methods] Find out the principles to make up those famous TCM prescriptions based on understanding the efficacy of medicine described in Shennong Bencao Jing, through combining comparing the original documents of each other with the clinical practice of Mr. Xu Xiaodong. The natural medicine such as Gan Dihuang, Baizhu and Chai Hu were used as mediums to relate those famous TCM prescriptions and Shennong Bencao Jing. [Results] The original documents of Shennong Bencao Jing and those famous TCM prescriptions which were related together by natural medicine such as Gan Dihuang, Baizhu and Chai Hu have much in common. For example, Gan Dihuang used in Si Wutang, Huang Tutang etc. according to the effect of promoting blood circulation and removing blood stasis described in Shennong Bencao Jing. Chang Pu used in Changpu Yujintang according to the effect of resuscitation and restoring consciousness described in Shennong Bencao Jing. Baizhu used in Fangji Huangqi Tang, Mahuang Jiazhu Tang of Jinkui Yaolue according to the antiperspirant effect described in Shennong Bencao Jing. Chai Hu used in Xiao Chaihu Tang, Chaihu Shugan San etc. according to the effect of relieving the abdominal discomfort, attacks of chills and fever described in Shennong Bencao Jing. The theory of Shennong Bencao Jing is well applied in clinical teaching and practice by Mr. Xu Xiaodong, bringing students a lot of inspiration. It is possible to explain the principles of making up those famous TCM prescriptions and guide the compatibility of TCM according to Shennong Bencao Jing. [Conclusion] Doctors in the ancient world have inherited and developed the Shennong Bencao Jing theory when filling the prescription; comprehension and application of those famous TCM prescriptions will be more original according to Shennong Bencao Jing. The theory of Shennong Bencao Jing is worth our further study and extension.