It is one of the top priorities to incorporate the well-being of graduate students into the training system to cultivate the top innovative talents in pharmacy. With the goal of improving psychological crisis recognition and intervention of graduate students majoring in pharmacy, this study selected 71 graduate students majoring in pharmacy in Shanghai Jiaotong University School of Medicine from April 2021 to May 2022 as research participants, conducted a questionnaire survey at important time points in training to identify possible psychological problems, adopted the method of combining individual psychological counseling and group psychological activities to explore the psychological health safeguard system (hereinafter referred to as the safeguard system) for pharmaceutical graduate students, including the postgraduate psychological committee, postgraduate management teachers, and school psychological consultants, and preliminarily evaluated the effect of the safeguard system construction for one year. The results showed that the safeguard system could identify the potential psychological problems of graduate students majoring in pharmacy at an early stage, and a total of 10 graduate students with potential psychological problems were detected. Individual psychological counseling and group psychological activities effectively prevented the occurrence of graduate students' psychological crisis, and alleviated 1 case of peer conflict, 3 cases of uneasy supervisor-postgraduate relations, and 6 cases of academic anxiety. Within one year after the establishment of the safeguard system, there are no graduate students dropping out of school (1 case in the previous year) or requesting tutor transfer (2 cases in the previous year). The construction of the safeguard system and its practical experience can provide empirical reference for the mental health education and crisis intervention identification of university graduate students.