Biodiversity conservation is of great significance for safeguarding national ecological security, conducting sustainable development, and participating in global governance. Since 2016, China has systematically implemented 52 holistic ecological conservation and restoration projects involving mountains, rivers, forests, farmlands, lakes, grasslands and deserts ("Shan-shui Projects" for short). These projects are all employed within the national ecological security barrier known as the “three zones and four belts”. The implementation of Shan-shui Projects has achieved certain progress in consolidating critical ecological barriers and protecting key species; however, no studies have yet systematically evaluated the rationality of their spatial layout from a biodiversity conservation perspective. Integrating the requirements of biodiversity conservation, this study assesses the spatial distribution characteristics of existing Shan-shui Projects, identifies priority areas for future projects, and aims to provide actionable references for advancing biodiversity conservation efforts. This study develops a county-level index for biodiversity conservation importance and priority in China, employing three indicators: the distribution of rare species at the county level, the degree of vegetation cover degradation, and the intensity of potential ecological stress. Furthermore, we have considered the important regions for biodiversity conservation, the layout of existing holistic projects and the distribution of national nature reserves, identifying the priority regions of future projects considering the needs of biodiversity conservation. The results show that: 1) Regions in China with high richness of rare species generally possess favorable ecological environments. There are 168 counties where the number of rare species is more than 100, among which only 24 counties exhibit vegetation cover degradation exceeding 20%. 2) The national important areas for biodiversity conservation are 3.93×106 km2, the overlapping area with 42 implemented holistic ecological conservation and restoration projects is about 6.4×105 km2, the rare species richness is mostly at medium level. 3) Currently implemented Shan-shui Projects are predominantly located in China's central and eastern regions. In the future, priority areas for holistic ecological protection and restoration projects that consider biodiversity conservation needs will include locations such as Daxing'an Mountains, the western and northern foothills of Tianshan Mountains, the Hengduan Mountains, and the Yunnan Plateau, etc.