Objective To evaluation the comprehensive acquired immunodeficiency syndrome (AIDS) intervention program conducting in men who have sex with men (MSM) population living in Inner Mongolia Autonomous region. Methods A comprehensive intervention program was carried out among MSM groups in Hohhot and Baotou City. Seven hundred and six and 767 MSM were enrolled for investigation through the snowball method during May 2008 and May to June 2009, respectively.At the same time, 5 mL intravenous blood sample was collected from each subject for human immunodeficiency virus (HIV) detection and intervention effect evaluation. Data were analyzed by x2test. Results After intervention, the awareness rate of HIV/AIDS knowledge increased from 70.7%(499/706) to 81.7%(627/767) (x2 =25. 004, P＜0.01 ). The rate of consistent condom use in the last six months increased from 38.0%(254/668) to 45.3% (346/764) (x2=8. 269, P＜0. 05). The percentage of subjects who had more than 5 different male sexual partner during the last 6 months significantly decreased from 42.8% to 24.6% (x2 = 55. 348, P＜0.01). The median number of sexual partners in MSM decreased from 3 in 2008 to 2 in 2009. The HIV infection rate was 1.7 % in both 2008 and 2009. Conclusion The comprehensive intervention program among MSM population shows positive influence after one year implementation, which is helpful for increasing HIV/AIDS awareness and safe sex behavior in this population.