Chinese medicinal formulae (CMF) were usually used in the clinics of traditional Chinese medicines (TCM), which were critical for modernization of Chinese medicine to shed light on the interaction between CMF and biological organisms. However, correlation between system and part, macroscopic actions and microcosmic mechanism, ADME process and pharmacologic actions were usually neglected. The put-forward of integrative pharmacology provided a feasible approach to solve the problem of the fragmentation of TCM. For the past years, we applied the strategy of integrative pharmacology to study Yuanhu Zhitong prescription( YZP) systematically, and established two modes, chemical fingerprints-metabolism fingerprints-network targets and intestinal absorption-activity evaluation-data mining, to establish the interaction rule between the chemical composition and biological activity from multiple levels, such as the calculation and in vitro/vivo, which provided proof for the quality control, pharmacodynamic material basis and pharmacological action of YZP. In this paper, we summarized the related progresses of the research of YZP.