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[Display omitted] • Species richness hotspots were identified by multi-species distribution modeling. • The magnitude and direction of future biodiversity hotspots changes were discussed. • The MaxEnt and InVEST models were complementary in biodiversity conservation. • Suggestions for biodiversity conservation were proposed based on gap analysis. Mainstreaming biodiversity into protection planning and management is of great significance for biodiversity conservation and sustainable development. Species potential distribution modeling is an effective way for species diversity evaluation and biodiversity hotspots identification, which are crucial for biodiversity conservation. Taking the Central Urban Area of Chongqing Municipality as the study area, the main objectives of this study were to identify the potentially suitable habitats, species richness and biodiversity of key protected species in current and future, determine the relative contribution of environmental factors and assess the conservation effectiveness of protected areas (PAs) based on MaxEnt model and gap analysis. The results showed that the current potentially suitable habitats of total key protected species were mainly located in "two rivers and four mountains", with a total area of 1610.55 km2, of which forestland accounted for 59.78 %. Species suitable habitats demonstrated clear topographic heterogeneity, and the distribution index decreased at first and then increased with increasing terrain niche index (TNI). Meanwhile, it was observed that key protected plants and birds shared similar suitable habitats in mountainous areas, with an overlapping area of 753.53 km2, and the high species richness covered 182.83 km2. In 2050, the future biodiversity hotspots would remain stable and increase steadily. In terms of the direction of centroid shift, the biodiversity hotspots would migrate to low latitude, low altitude and southeast by 8.34 km. The jackknife tests indicated that the potential distribution of key protected species was mainly determined by land use, mean diurnal range and TNI. Additionally, the problems of high protection gaps and low protection effectiveness coexisted in the existing PAs, with the overlapping area of the comprehensive biodiversity hotspots and the existing PAs was only 446.96 km2. Finally, suggestions for natural PAs system optimization and ecological protection were proposed. This study provides scientific supports for biodiversity conservation and efficient management. [ABSTRACT FROM AUTHOR]