Traditional Chinese Medicine (TCM), as an important component of complementary and alternative medicine, has become well known for its significant role in preventing and treating breast lesion with nipple discharge (ND). In the present study, the ND and serum biomarkers level of cancer antigen 153 (CA153) and carcinoembryonic antigen (CEA) were measured and compared with the express of Hypoxia inducible factor-1α (HIF-1α) and nuclear proliferation index Ki-67 in tissue in 93 breast intraductal papillary leision patients with ND, of which, 29 patients diagnosed with intraductal papillary carcinoma received Western medicine EC-P chemotherapy program combined with Runiu recipe TCM treatment. We investigated the significance of TCM as an adjunctive therapy and analyzed the relationship with the levels of biomarkers and clinical outcomes in papillary carcinoma. The results shown that the expression of HIF-1α and Ki-67 in breast papillary carcinomas were higher than those in benign lesions and positivity correlated significantly with ND levels of CA153 and CEA in papillary carcinomas (p<0.05, respectively). TCM combined with Western medicine can relieve the clinical Chinese medical symptoms of papillary carcinoma patients, and decrease CA153 and CEA levels (p<0.05, respectively). This study suggests that HIF-1α, Ki-67, CA153 and CA125 may be considered as potential marker of Western medicine EC-P chemotherapy program combined with TCM therapy evaluation for breast lesions with ND.