Objective To investigate the molecular mechanism of Danpu Capsules in treating chronic prostatitis pelvic pain. Methods The rat model of improved experimental autoimmune prostatitis was established，then the rats were randomly divided into large-dosage，medium-dosage and low-dosage Danpu Capsules groups，Qianleitai group，model group. After 8-week medicine administration the rats were killed and the prostate tissue was taken for the observation of histomorphological changes of prostate with the light microscope in all groups. The COX-2 level of prostate tissue and serum was detected by enzyme-linked immunosorbent assay（ELISA） and the expression of COX-2-mRNA in prostate was determined by real-time reverse transcriptase polymerase chain reaction（RT-PCR）. Results The result of ELISA showed that the COX-2 level of the model group was higher significantly than that of the normal group（P<0. 01）. After large and medium doses of medicine administration the COX-2 level of the Danpu Capsules group was decreased significantly（P<0. 01）. The result of RT- PCR showed that the rat model of autoimmune prostatitis had higher expression of COX-2-mRNA，while in the large and medium doses of Danpu Capsules group this expression was inhibited（P<0. 01）. Conclusion 1 The improved EAP rat model is successful. The mechanism of treating autoimmune prostatitis with Danpu Capsules maybe related to that Danpu Capsules can inhibit COX-2 expression.