Objective To analyze the innovative ability of medical postgraduate students who have won national scholarships, and discuss the cultivation of innovative ability of clinical medicine postgraduate students and related factors. Methods A survey was based on the 2016 and 2017 postgraduate students majoring in clinical medicine at West China School of Medicine of Sichuan University. According to whether they had won a national scholarship, they were divided into a national scholarship group and a control group. The innovation ability and cognitive differences of the two groups of postgraduate students were compared, and related factors were explored. Results A total of 1 173 valid questionnaires were responsed, with a response rate of 80.23%. There was no statistically significant difference in gender and major between the two groups of postgraduate students (P>0.05). For master’s degree postgraduate students, the proportion of published papers in international medical journals (80.95% vs. 29.63%), published high impact factor (impact factor≥6) journal papers (7.84% vs. 6.16%), applied for research patents (12.70% vs. 3.51%) and innovation and entrepreneurship competition awards (20.63% vs. 3.93%) in the national scholarship group were higher than the control group, the differences were statistically significant (P<0.05). For doctor’s degree postgraduate students, the proportion of published papers in international medical journals (96.00% vs. 69.66%), published high impact factor journal papers (22.22% vs. 8.89%), applied for research patents (17.33% vs. 8.36%), and innovation and entrepreneurship competition awards (17.33% vs. 1.86%) in the national scholarship group were higher than the control group, the differences were statistically significant (P<0.05). Regarding the cognition of the composition of innovation ability, the differences between the national scholarship group and the control group were not statistically significant (P>0.05). Regardless of master’s degree or doctor’s degree, more than 40% of the postgraduate students in the national scholarship group and the control group believed that the most important factor in the personal influence of innovation ability was the knowledge factor, and more than 45% of the postgraduate students believed that the most important factors affecting the cultivation of innovative ability was their own factors or tutors’ factors. Conclusions The innovative ability of clinical medicine postgraduate students needs to be improved. The level of tutors’ scientific research ability, tutors’ guidance, high-quality scientific research team, and a good academic atmosphere play an important role in the cultivation of innovation ability. Optimizing the team of tutors, forming a scientific research steering group, building a high-level innovation platform, aiming at publishing high-level papers, strengthening domestic and foreign exchanges and cooperation, and motivating students to participate in innovation and entrepreneurship competitions are powerful measures to cultivate innovative medical talents.