To establish potent fingerprint for quality control of traditional Chinese medicine, Houttuynia cordata (Saururaceae) injection (HCI), the attempt on fingerprint-efficacy was developed in this study. HCI from ten different factories were determined by gas chromatography-mass spectrum (GC-MS) and classified by hierarchical clustering. The anti-inflammatory effect of HCI was characterized with the rat pleurisy model induced by carrageenin and the mice ear edema model by xylene. The results showed that anti-inflammatory effect of the injections from most of factories on the two models was significant. There was corresponding relationship between the fingerprint of HCI and efficacy to certain extent. The main common constitutes in injection from the factories that possess anti-inflammatory activity were analysed with GC-MS and identified using the NIST Mass Spectral Database. This common pattern of HCI based on the efficacy was helpful for the purpose of quality control.