Performance evaluation of human resources management is important for promoting the development of pharmaceutical enterprise, and the application of fuzzy comprehensive evaluation on it is studied in depth. Firstly, the existing problems in performance evaluation of pharmaceutical enterprise are analyzed. Secondly, the construction principles of performance evaluation for human resources management are discussed. Thirdly, the basic theory of fuzzy comprehensive evaluation is studied. Finally, a case study is analyzed, results show that the fuzzy comprehensive evaluation is an effective method for evaluating the human resources management level of pharmaceutical enterprise