Objective The structural equation model (SEM) was used to analyze the data of psychological scales to explore the effects of these on willingness to use and adherence to HIV pre-exposure prophylaxis (PrEP) among men who have sex with men (MSM), and to provide the basis for effective implementation of PrEP intervention strategy among MSM in China. Methods Online recruitment and time-location sampling (TLS) were used to recruit MSM in Nanjing. Questionnaire survey was filled by Questionnaire Star software. Three psychological factors of anticipated HIV stigma, community homophobia and depressive symptoms were included in the SEM to explore the mechanism of these interaction with willingness to use and adherence to PrEP among MSM. Results 75.73% of participants were willing to use PrEP and 55.34% were self-reported high intention to adhere to PrEP. Participants had high anticipated HIV stigma and community homophobia, with median 20 (17~23) and 27 (22~30), respectively, but had few depression symptoms, with median 1 (0~2). Anticipated HIV stigma had a direct positive effect on willingness to use and adherence to PrEP, with effect sizes of 0.13 (P<0.05) and 0.14 (P<0.05), respectively. Community homophobia negatively predicted PrEP adherence (β=-0.15, P<0.05). Depression symptoms played a partially mediating role between community homophobia and PrEP adherence, with an effect size of 0.03 (P<0.01). Conclusion High willingness to use PrEP, but low drug adherence were indicated among MSM. Psychological factors had significant effects on the willingness to use and adherence to PrEP. Psychological services should be in conjunction with PrEP prevention and intervention strategies to achieve better benefits of PrEP. Kew words structural equation model; pre-exposure prophylaxis; men who have sex with men; psychological factors