This study aimed to explore the awareness, willingness, and engagement with pre-exposure prophylaxis (PrEP) among high-risk Chinese men who have sex with men (MSM) and to investigate the factors influencing its use. A cross-sectional survey of 1800 HIV-negative MSM was conducted in Chengdu, Suzhou, and Wuhan between June 2022 and February 2023 through in-person and online recruitment methods. Univariate and multivariate logistic regression analyses were used to identify predictors of PrEP use. Bayesian network models were constructed using the bnlearn package in R 4.1.2, and inference was conducted using Netica software. Among the 1800 participants, 1467 had ever heard of PrEP, 696 were aware of its target population, and 195 had taken PrEP in the past 6 months. PrEP use was higher among individuals reporting multiple male sex partners, illicit substance use, alcohol use, HIV testing, PEP use, and sexual partners who had used PrEP. Conversely, having a female sexual partner was a barrier to PrEP use. Bayesian network modeling unveiled factors directly and indirectly impacting PrEP use. Variables like PrEP use of sexual partners, PEP use, alcohol use, HIV testing, and WeChat-based HIV knowledge platforms exhibited direct effects. Indirect effects included having a female sexual partner, number of male sexual partners, and illicit substance use. Despite high awareness, the usage of PrEP remains low among MSM. Encouraging social agencies to leverage social media platforms to provide comprehensive HIV care services, especially to meet the PrEP needs of MSM.