The paper presented the application advance of mass spectrometry techniques on Chinese medicine research from three aspects: the component analysis, bio-activity screening and metabonomics research. The section of the component analysis focused on various methods for analyzing oligosaccharide isomers. And the applications of the fingerprint technique of mass spectrometry to the component analysis and quality control of Chinese medicine were also provided. On the research of bioactivity compound screening, some techniques were introduced respectively, including the ultrafiltration-mass spectrometry, cell membrane chromatography-mass spectrometry, microdialysis probe-mass spectrometry, affinity chromatography-mass spectrometry, intensity-fading mass spectrometry, modified agarose-mass spectrometry and direct analysis mass spectrometry, etc. On the metabonomics studies, we provided some examples which clarified the action mechanism of Chinese medicine on hepatotoxicity, kidney deficiency, myocardial infarction and type 2 diabetes. The above content reflected the importance of mass spectrometric techniques in the innovative research of Chinese medicine.