The protected area has high biodiversity and vital important ecological benefits, such as water conservation, soil and water conservation, sand fixation and wind prevention. In Beijing, the protected area are the core of the capital's ecological barrier. There are still many problems in the management of the protected area management, and human disturbance(population, economy and transportation) is prevalent, which seriously affects the ecological benefits of the protected area, especially in big cities such as Beijing. The natural factors also have impacts on ecological benefits of the protected area. However, there is still a gap in the understanding of the main factors the affecting the ecological benefits of the protected area in Beijing. We calculated 5 typical ecological benefits of 79 natural protected areas in Beijing, and compared the difference of ecological benefits of 5 types of protected area (natural reserve, forest park, scenic and historical interest area, geopark and wetland park) with one-way ANOVA. The effects of two natural factors (annual average temperature and annual precipitation) and four human impacts (population density, proportion of construction land, proportion of cultivated land and road density) on ecological benefits were investigated based on redundancy analysis. The results showed as follows:(1) in 2020, the value of water conservation per unit area in Beijing's protected areas was 34347 yuan/ha, the value of wind prevention and sand fixation was 2774 yuan/ha, the ecological value of soil and water conservation was 1274 yuan/ha, and the carbon fixation value was only 473 yuan/ha. In addition, the mean value of habitat quality per unit area in Beijing's protected areas was 0.88. (2) While comparing ecological benefits among different types of protected area, except habitat quality, the total benefits of the other four types of ecological benefits, nature reserve and forest parks were significantly higher than the other three types of natural protected areas. The habitat quality of wetland parks was significantly lower than that of the other four types of protected area, and there was no significant difference among the four types of protected area. In terms of ecological benefits of water conservation, scenic and historical interest area and geoparks were significantly lower than other three types of natural protection area. (3) Compared with natural factors (16.63%), human factors (38.92%) were the main factors affecting the ecological benefits of the protected area in Beijing, mainly including wind prevention and sand fixation, soil and water conservation and carbon fixation. Habitat quality was affected by both natural and human impacts, and water conservation was mainly affected by natural factors. ('4) Based on redundancy analysis (RDA), all the protected area in Beijing could be divided into three types:water conservation type, high-quality habitat type, and other ecological benefits (including wind prevention and sand fixation, water and soil conservation and carbon sequestration). The results showed that it was important and urgent to integrate and optimize the protected area in Beijing, and the key point was to reduce the construction and agricultural land in the protected area, and move excessive population out of the protected area. This study was of great significane to improve the ecological benefits of the protected area in Beijing, and provides theoretical and technical support for the scientific management of the protected area in Beijing.