Background Desert nature reserves are important ecological security barriers in arid and semi-arid areas of Northwest China. However, the existing desert nature reserves are partially overlapped and unevenly distributed, and the important desert natural ecosystems and biological species have not been effectively protected. Therefore, this study aims to systematically investigate and divide the natural ecological protection space in China's deserts, scientifically identify the protection gaps of each natural geographical region, and optimize the spatial layout by zoning and grading, so as to provide a reference for the rational spatial layout of China's desert nature reserves and maintaining the stability of desert ecosystems.

Methods Based on ArcGIS spatial analysis, mathematical statistics and GAP analysis, with China's terrestrial desert regions and current nature reserves as subjects, the natural protection in deserts was geographically divided, the key areas for the construction of nature reserves were identified, as well as the protection gaps and geographical units with low protection effectiveness in desert nature reserves were analyzed and evaluated through the division of current nature reserves, natural geographical areas and various relevant special divisions combined with the integrity of desert landform, the difference of desert vegetation distribution and the spatial layout of nature reserves. On this basis, the layout plan for China's desert nature reserves was optimized.

Results 1) The natural protection of deserts was geographically divided into 5 zones, 17 sub-zones and 58 small zones. There were 23 protection gaps in the natural ecological protection space of the deserts. 2) The background data of 40 desert nature reserves in China were constructed, with a coverage of 41×10⁶ hm², accounting for 27.83% of the total area of the national nature reserves, accounting for 9.14% of the total area of the deserts in China, and protecting 9.89% of the important natural ecosystems in the deserts. 3) National desert nature reserves were mainly distributed in the Qiangtang Block of the Qinghai-Tibet Plateau, the Kunlun Mountains and the Alxa Block and Hexi Corridor of the Northwest Plateau-Basin, presenting a trend of higher land coverage in the west and lower in the east in each province. 4) The optimized layout plan for desert nature reserves in deserts was proposed. It was suggested that 15 desert nature reserves should be newly built firstly, 1 promoted, 2 merged, 2 cancelled and 7 conversed. After optimization, there were 45 desert nature reserves, with an area of 44.08×10⁶ hm².

Conclusions The optimized layout will fill in or improve the protection proportion of 9 small nature reserves in China's deserts, increase the protection proportion of the deserts from 9.14% to 9.83%, and enhance the priority protection of desert ecosystems from 9.89% to 14.47%, which solves the contradictions of overlapping, unreasonable spatial layout and unclear protection targets of the nature reserves in the deserts. Moreover, it will improve the systematic protection of fragile desert ecosystems and national key protected wildlife.