 The research field of systems biology has led to the development of network pharmacology, which is more effective for establishing a compound protein slash gene disease network and revealing the regulation principles of small molecules in a high throughput manner. This approach makes it powerful for analyzing drug combinations, especially traditional Chinese medicine, TCM, preparations. The work summarizes TCM databases and tools, focuses on several representative applications of network pharmacology for TCM research, compares the general statistics of current TCM databases, evaluates search results based on 10 famous herbs, and suggests future studies should focus on both the microbiome and TCMs to better understand and treat microbiome-related diseases. This article was authored by Ruan Zhijian, Shui Zhu, Hong Bai, and others.