BACKGROUND: Behavioral intervention is a key approach to HIV prevention among men who have sex with men (MSM). Widespread use of mobile phones provide us with novel opportunities to decrease HIV infection and transmission of MSM. The objective of the study was to design and develop a mobile phone application (app) aims to conduct behavioral intervention to MSM and to evaluate the efficacy of the app-based intervention compared to usual care, to analyze cost-effectiveness and mechanism of the intervention. METHODS: This study involves 2 phases, phase 1 use qualitative method and phase 2 is a randomized controlled trial lasting for 18 months, they will be conducted in Chagnsha, Hunan Province, China. Phase 1 is to design and develop the app, procedures including retrieval of domestic apps related to prevention and treatment about HIV and sexually transmitted diseases (HIV/STDs), personal interviews with MSM about preferences and functional needs of the HIV prevention app, multidisciplinary experts focused group discussions of the app, software engineers' development and users test of the app will be performed. In phase 2, we will recruit 800 MSM by cooperating with the local center of disease control and prevention and nongovernmental organizations, and divide them into intervention and control group evenly. Intervention group participants will receive app-based HIV prevention. Control group participants will be provided with usual care including HIV/STDs knowledge brochure and free voluntary counseling services. Data will be collected at baseline, 6, 12 and 18 months since subject's participation. Effectiveness of the intervention includes HIV/STDs infection rates, adherence to regularly HIV testing, sexual risk behavior, consistent condom use and relative risk of HIV infection. Cost-effectiveness will be analyzed by decision-analytic modeling, and mechanism analysis of this app-based intervention will be performed by path analysis. DISCUSSION: This will be the first study of its kind in China to develop an app and implement app-based HIV prevention intervention among MSM. It is of great potential to determine whether app-based intervention is a cost-effective way to decrease HIV infection among MSM and explore intervention mechanism with an accurate method. TRIAL REGISTRATION: Chinese Clinical Trial Register ( ChiCTR-IOR-15006724 ). Registered 10 July 2015.