Currently the national average prevalence of human immunodeficiency virus (HIV) in China remains low, but HIV infection rate among men who have sex with men (MSM) increases rapidly. The HIV subtypes spreading in MSM show new features and the disease progression of HIV-infected MSM is fast. The detection of HIV nucleic acid, antigen and antibody play important roles in the early identification of HIV-infected MSM. Investigating the factors affecting HIV infection progression and looking for the new biomarkers can provide novel strategies for early prediction of HIV infection prognosis. The early identification and interventions such as antiretroviral therapy in HIV-infected MSM are important in the control of HIV epidemic in China.