[Objective] The functional structure of the watersheds was quantitatively analyzed， and the influencing factors on the development of the watersheds were explored, in order to comprehensively understand the efficacy of constructing ecologically clean watersheds in the mountainous areas of Northern Beijing City, and provide a theoretical basis for the comprehensive management and development of the watersheds in the mountainous areas. [Methods] The small watersheds in Diaoliushi, Yushuidong, Gubeikou, and Huluhe River in the Yanqing, Huairou, Miyun, and Changping Districts, respectively, were selected as representative areas, and the main characteristics and governance objectives of each area was combined to construct a comprehensive benefit evaluation index system for these small watersheds in the mountainous areas of Northern Beijing City. The comprehensive benefit evaluation of the small watersheds was conducted via an analytic hierarchy process and weighted comprehensive index method, and the main influencing factors of constructing ecologically clean watersheds were revealed by the systematic obstacle degree model. [Results] ① Different results were found for the comprehensive management of each small watershed. The Hulu River watershed was upgraded from the primary to intermediate standard, and the comprehensive construction of the Zhujiushi, Yushuidong, and Gubeikou watersheds reached the primary standard. ② The obstacle degree model, which was introduced to quantify the contribution of different influencing factors, provided accurate evaluations. ③ In the future development process of small watersheds in the mountainous areas in Northern Beijing City, attention should be paid to the soil erosion modulus, economic production ratio and land productivity, Engel coefficient (household food expenditure ratio) and the proportion of rural employees, and the chemical oxygen demand (COD) content for the ecological, economic, social, and water-quality improvement benefits, respectively. [Conclusion] ① The comprehensive benefit evaluation system of small watersheds proposed in this study is practical and feasible in the mountainous areas in Northern Beijing City. ② Through the management of ecologically clean watersheds, the water environment and soil erosion were effectively controlled, the industrial structure in the watersheds was gradually enhanced, the ecological and human settlements were improved, and the coordinated development of soil and water resources, ecological environment, and economy and society were promoted.