The decline in biodiversity poses a serious threat to natural ecosystems and has become one of the most pressing global environmental issues. Establishing conservation priorities for protected areas (PAs) is one of the most direct and effective biodiversity conservation measures. However, conservation gaps arise as a result of existing problems in spatial layout of PAs, including overlapping protection scopes, artificial fragmentation of natural ecological regions, as well as "over-protection" and "over-exploitation." To optimize the spatial layout of PAs and improve the efficiency of biodiversity conservation, we employed the Habitat Quality module of the Integrated Assessment of Ecosystem Services and Tradeoffs (InVEST) model and the Maximum Entropy (MaxEnt) model to assess the PAs in the Songnen Plain, China. The combined model (MaxEnt-InVEST) revealed that the conservation priorities for PAs in the Songnen Plain occupied a total area of 14,764.14 km2 (10.24% of the total area of the Songnen Plain). The conservation priorities outside PAs occupied a total area of 7858.45 km2 (5.45% of the total area of the Songnen Plain) and were primarily distributed in the northeastern, central, and southwestern regions of the Songnen Plain. This indicated that existing PAs did not offer adequate protection for local biodiversity. The consistency of our combined modeling framework was 72.11%, which enabled a more accurate assessment of biodiversity hotspots and respects the land uses of the Songnen Plain. In addition, the modeling framework successfully created maps of conservation gaps of biodiversity hotspots based on actual species distribution data and considers current land uses. Our study was aimed at optimizing the spatial conservation efficiency of the Songnen Plain by assessing the conservation gaps in the Songnen Plain. It could provide a reference for the future development of a PA system centering on national parks.