Habitats are essential for the survival of wild animals, and clarifying the distribution of a species' suitable habitat can be helpful to strengthen wildlife conservation and to increase the conservation effectiveness for biodiversity. As the capital of China, Beijing holds abundant wild animals and the government has established different types of natural protected areas to provide the refuge for the wildlife. Nowadays, it is urgent to assess the effectiveness of these natural protected areas on the protection of habitats of the wild animals, which will provide scientific guidance to wildlife conservation management and integration of natural protected areas in Beijing. Based on the relative importance and the availability of the distribution data, we selected 6 typical wild animals in Beijing, i.e., Black stork (Ciconia nigra), Brown eared-pheasant (Crossoption mantchuricum), Great bustard (Otis tarda), Mandarin duck (Aix galericulata), Golden eagle (Aquila chrysaetos) and Chinese goral (Naemorhedus griseus), and collected the distribution data of these species through field investigations, open databases and literature. We then analyzed the suitable habitats using the MaxEnt model and spatial analysis function of ArcGIS. We also identified the hotspots and GAPs (GAP analysis) of these species' suitable habitats in Beijing. The results indicated that the natural protected areas covered various proportions of these animals' suitable habitats with a range from 13.66% (Mandarin duck) to 92.82% (Brown-eared pheasant). The total area of the suitable habitat hotspots was 280.01 km², and mainly distributed in Miyun District, Yanqing District, Mentougou District and Fangshan District. However, the coverage of species hotspots differed among different natural protected areas, with it being highest in scenic spots (14.74%). The GAPs were responsible for 49.45% of the hotspots and mainly distributed in Miyun District, Mentougou District, Fangshan District, and the border of Miyun, Huairou and Yanqing. In particular, Miyun District, Mentougou District and Fangshan District held the largest areas of GAPs. Based on the distribution of the suitable habitats and the protection gaps, it is suggested to take suitable measures to improve the conservation effectiveness of the natural protected areas according to the local circumstances, and adopt different protection strategies for different protection objects, including expanding or merging some natural protected areas, establishing new natural protected areas, and creating micro-habitats. Our study provides feasible solutions for the identification and delineation of important wildlife habitats in Beijing, provides some scientific guidelines for the wildlife management and integration and optimization of the natural protected area system.