Objective To construct the evaluation system of faculties' ideological, political and professional ethics in school of pharmaceutical sciences. Methods The literature research method was used to determine the evaluation indicators, evaluation patterns, and evaluation processes preliminary. Delphi method were used to conduct subsequent two rounds of expert consultation to 18 experts. Results The effective questionnaire response number for both rounds of expert consultation was 18. The coefficient of variation of evaluation indicators for the second round of consultation was less than 17.5%, Kendall's coordination coefficient was 0.388 (P<0.001), Cronbach's α was 0.682. Seventeen or more experts agreed on the evaluation method, and all experts agreed on each type of evaluation process. An evaluation index consisting of 6 primary indicators and 33 secondary indicators have been formed; five evaluation methods selected for different secondary indicators have been determined; five evaluation processes have been determined after adjusting and optimizing according to expert opinions. Conclusions The evaluation system for the ideological and political education and professional ethics of faculties in school of pharmaceutical sciences is relatively comprehensive, effective, and easy to implement, which provide a reference for the evaluation of the ideological and political education and professional ethics of faculties in secondary schools/colleges of universities.