Objective To investigate the mental health status of newly-enrolled “3+2” assistant general practitioner program students. Methods The investigation started in February 2017 covered 375 newly-enrolled “3+2” assistant general practitioner program students to complete university personality inventory (UPI) from 2017 to 2019, and rank sum test and chi-square test was used to analysis data. Results Students who were highly potential to have serious psychological problems (Type Ⅰ) take 15.5%(58/375), students who were possible to have general mental issues (Type Ⅱ) take 22.1%(83/375) , students who were relatively mentally healthy (Type Ⅲ) take 62.4% (234/375). UPI score of male was 3.00(1.00,9.00), female was 4.00(1.00,10.75), grade 2017 was 4.00(1.00,12.50), grade 2018 was 4.00(1.00,10.00), grade 2019 was 3.00(1.00,8.00), Daxing was 7.50(2.00,19.25), Pinggu was 3.00(1.00,10.00), Tongzhou was 6.00(1.00,11.00), Mentougou was 2.00(1.00,4.00), Huairou was 9.00(3.00,13.00), Miyun was 4.00(1.00,11.50), Yanqing was 3.00(1.25,8.25), Changping was 4.00(1.00,10.25), Shunyi was 3.00(1.00,8.00), Fangshan was 2.00(1.00,7.00). No significant difference was found among students enrolled from 2017 up to 2019, between male and females and different districts(all P>0.05). Conclusions Most of “3+2” assistant general practitioner program students had good mental health, and it was similar in different gender, grade and district. For the students of “3+2” program, we should give highly concern and construct stable mental health system, provide special consulting service according to students' metal health features.