To determine the prevalence and relative factors on those who missed the follow-up service among newly reported HIV/AIDS cases that were infected by homosexual behavior. Data were extracted from both HIV/AIDS case-reporting and follow-up cards on HIV/AIDS in the Comprehensive Response Information Management System, between December 2008 and December 2015. Data was analyzed, using the generalized estimating equations (GEE) to explore the relative factors of influence. Among the newly reported HIV infection among MSM, the proportion of those who missed the follow-up services was 5.06% (6 037/119 358), and decreased dramatically, from 37.57% (1 261/3 356) to 0.84% (267/31 935) (trend (2)=103.43, <0.01). In MSM population, the younger than 20-year olds (=1.30, 95%: 1.11-1.52), 20-year olds (=1.52, 95%: 1.36-1.69), 30-year olds (=1.22, 95%: 1.12-1.34), 40-year olds (=1.10, 95%: 1.01-1.20) were receiving less follow-up services than those 50-year olds. Those who had received either junior (=1.52, 95%: 1.37-1.69) or senior high school education (=1.35, 95%: 1.23-1.49) were receiving less follow-up service than those who were more educated. MSM with the following characteristics as unspecified occupation (=2.06, 95%: 1.49-2.87),unemployed (=1.54, 95%: 1.30-1.83), working in commercial service (=1.31, 95%: 1.15-1.49) or being student (=1.34, 95%: 1.18-1.52) were more difficult to be traced or followed than the cadres. Cases being identified on site (=2.99, 95%: 2.26-3.95) or under special investigation (=1.43, 95%: 1.29-1.59) had received less follow-up service than those being identified through voluntary counsel testing service. Floating population (=1.46, 95%: 1.28-1.66) were getting less follow-up service than local residents. The prevalence of those who had missed the follow-up services in the newly discovered MSM HIV cases declined dramatically. Among the MSM HIV cases, those having the following characteristics as: younger than 50-year old, with less school education, with unspecified occupation or unemployment, working in commercial service, being student, having history of incarceration, recruited from special investigation, and floating population were prone to miss the follow-up program, suggesting that the follow-up service should be targeting on these patients.