Irrational spatial patterns are one of the main problems for nature reserve development. Optimization of current nature reserve systems is one of the best approaches for achieving maximal conservation biodiversity effectiveness with limited conservation resources. In this study, habitat evaluation and priority identification were undertaken in the Minshan Mountains in southwest China, one of the most important areas for biodiversity conservation in the world. A total number of 25 endangered species, including 15 mammals and 10 birds, were selected to identify priority areas based on MAXENT and ZONATION, which were further used to optimize the current nature reserve systems. In total, 3213 occurrence points for the 25 species, and several environmental variables, including the Wide Dynamic Range Vegetation Index from MODIS data, slope and aspect from DEM data, and distance to roads and residential areas, were selected for habitat modeling. The results showed that(1) MAXENT could predict the distributions of study species well with relatively small numbers of occurrence records;(2) Average ratio for the 25 species' habitats in the current nature reserve systems was 51.8%;(3) The total area of the priority areas was 19958.7 km², only 47.1% of which had been protected in the existing nature reserves, and protection gaps existed in the middle and south of Jiuzhaigou County, the north of Pingwu County, and the border between the southwest of Pingwu County and the Northeast of Beichuan County. Therefore, it was proposed to build new nature reserves or expand the existing nature reserves in 6 protection gap areas, and to take the priority rank within the areas into account during future planning. After expansion of the reserves in the six key areas, the proportion in new nature reserves to the entire area will increase to 33.3% from the current 23.8%.The average ratio for the 25 species could be raised to 77.9%, with a net increase of 26.1% compared to the current ratio. Finally, species with small habitat areas will have a high proportion of habitat protected in the new reserve planning regime. The approach used in this study could be applied to other biodiversity hotspots in China.