Traditional Chinese medicine(TCM)compatibility is related to the safety of clinical use of drugs and embodies the essence of interactions between drugs and organisms. This is a scientific problem thatr has attracted more attention. Currently, most of the knowledge on TCM compatibility is from predecessors′ experience. The corresponding molecular biology mechanism is poorly understood. As a powerful tool to identify a large number of proteins simultaneously,proteomics technology has the potential to reveal the protein alterations under certain conditions,and to provide more direct insights into biological processes during TCM compatibility. In this paper,we introduced the main technology of proteomics,including two dimensional gel electrophoresis,2D-DIGE,iTRAQ, QconCAT/MRM and chemical proteomics. Also,the applications of these technologies in the field of TCMM compatibility study were reviewed.