Objective To explore the medication rule of TCM prescriptions in the treatment of HIV/AIDS related diarrhea, so as to provide references for clinical medication and TCM new drug and hospital preparations research. Methods Clinical research literature on the treatment of AIDS related diarrhea with TCM methods were collected and analyzed from CNKI, VIP and Wanfang databases from the beginning to 2019. All the relevant prescriptions in the literature were collected, and a database was established accordingly. Using data mining methods of Traditional Chinese Medicine Inheritance System (V2.5), use frequency, drug pairs, efficacy, and compatibility rule were analyzed, and new prescriptions were developed. Results A total of 48 prescriptions for AIDS related diarrhea were collected and screened out. In these prescriptions, the most frequently used herbs were Baizhu, Gancao, Fuling, Huanglian, and Dangshen etc, and the most frequently used drug pairs were Baizhu-Fuling, Baizhu-Gancao, and Dangshen-Baizhu. Drug pairs with confidence of 1 in the association analysis included Fuling→Baizhu, Gancao and Fuling→Baizhu, Dangshen and Fuling→Baizhu. Finally, with cluster analysis, 10 core drug combinations were found, and 5 new prescriptions were developed. Conclusion TCM treatment of AIDS related diarrhea is generally based on the principle of invigorating the Spleen and Qi and promoting water and dampness. The efficacy of new formula mainly focus on warming the Spleen and Kidney and drying dampness and relieving diarrhea, which provides certain reference for the further research in the future.