OBJECTIVE：To explore the problems and improvement measures in the process of operation and management of B2C pharmaceutical E-commerce enterprise，and to promote their development. METHODS：The performance evaluation index system was built preliminarily，including 5 first-level indexes and 28 second-level indexes. Questionnaires survey was conducted among 16 experts by Delphi method，and the weight of every index was calculated by experts according to importance，familiarity and reference. The company performance was analyzed and judged objectively by fuzzy comprehensive evaluation method. The results of Y enterprise performance evaluation were empirically analyzed. RESULTS & CONCLUSIONS：The performance evaluation index system has been built，including 5 first-level indexes，24 second-level indexes. Average expert authority degree of two rounds survey is 0.76（＞0.70），showing survey result is credible. The performance of the company in the finance and popularization have more influence to the performance of B2C pharmaceutical E-commerce enterprise. The performance of Y company is outstanding in profit growth，site stability and security，suppliers development and maintain and other aspects；however，it is not good enough of performance in employee satisfaction，customer professional services，logistics and distribution quality and other aspects. It is suggested to establish logistics by B2C pharmaceutical E-commerce enterprise themselves，carry out whole-course monitoring to improve the quality of logistics and distribution；increase product and pharmaceutical knowledge training input and introduce talent with the background of medical education so as to strengthen professional service；survey the satisfactory degree of staff to working environment，working group，working content and other aspects，and adjust enterprise system or communicate with staff in order to improve satisfactory degree.