Men who have sex with men (MSM) in China face high rates of HIV and syphilis infection exacerbated by internal migration. Studies on the differences of HIV and syphilis epidemics changing trends in high-risk behaviors and geographic distribution between resident and migrant MSM in Jiangsu, China were conducted. MSM were recruited from 14 surveillance sites in the serial cross-sectional study. Data on demographics, sexual behaviors, HIV and syphilis prevalence were collected. Participants were classified as residents or migrants based on household registration. During 2010-2014, 19,750 MSM were investigated. Engaged in anal sex (76.3% to 80.2%, P < 0.01) as well as received HIV-related services (72.1% to 79.2%, P < 0.01) were increasing. In contrast, engaged in commercial anal sex with males (7.4% to 5.0%, P < 0.01) and drug use (1.6% to 0.8%, P < 0.01) were decreasing. HIV prevalence ranged between 8.6% to 9.6%, while syphilis prevalence decreased over time (13.4-6.8%, P < 0.01). Further, we found that migrant MSM were more likely to engage in condomless anal sex, also had a higher HIV and syphilis prevalence than resident. During the study period, while syphilis prevalence decreased, higher rates of risk behaviors among migrant MSM called for targeted intervention strategies to reduce the HIV transmission.