Protected area are the cornerstone of biodiversity and ecosystem service conservation at the local, regional, and global levels. In 2019, China proposed the establishment of a nature reserve system (NRS)centered on national parks, integrating and improving various existing protected areas. This study focuses on the Qinling‒Daba Mountains, an area crucial for both biodiversity and ecosystem services. Through assessments of carbon storage (CS), water yield (WY), soil conservation (SC), and habitat quality (HQ), different conservation scenarios are considered in the context of Systematic conservation planning (SCP). An optimization scheme for the NRS in the Qinling-Daba Mountains is proposed, incorporating ecosystem services and comparing them with the existing system. Research indicates that the main protected areas are concentrated in the Min Mountain‒Motian Mountain‒Longmen Mountain region, the central Qinling region, and the Shennongjia‒Daba Mountain region. Compared with the original system, the area of protected regions in the NRS expanded by 52,000 km