The epidemic of HIV/AIDS among Chinese men who have sex with men is rapidly escalating. We implemented partner notification among HIV infected men who have sex with men cooperating with men who have sex with men-serving community-based organizations in two Chinese cities from June 2014 to May 2015. Community-based organizations participated in identifying new HIV-positive men who have sex with men utilizing rapid HIV tests and partner notification among index cases. Totally, 253 index cases were recruited and 275 sexual partners were notified and tested with 10.5% screened positive. Compared with previously identified index cases, the proportion of contactable sexual partners of newly identified index cases was higher but the testing rate was lower (p < 0.001). In all, 83.7% of sexual partners were casual with a contactable rate of 24.9% and a HIV testing rate of 71.1%. Having no contact information for sexual partners and fear of disclosure of HIV status are the main reasons for declining partner notification. It is feasible and effective to perform partner notification cooperating with community-based organizations among Chinese men who have sex with men.