Objectives Qinghai Province safeguards China’s “Water Tower” and serves as a vital ecological security barrier and repository of alpine biological genetic resources in western China. Investigating the natural protrected area system in Qinghai, primarily composed of national parks, holds significant importance for the development and reform of national parks and nature reserves. The study also provides valuable insights into the ongoing construction of provincial natural protected area systems, with a focus on national parks.

Methods This study examined the 95 natural protected areas in Qinghai Province, categorized into 7 types. It employed methods such as the nearest-neighbor index, kernel density index, and spatial overlay to analyze the spatial clustering and overlapping characteristics of the provincial natural protected area system. Utilizing mathematical statistics and ArcGIS spatial analysis techniques, the study identified the natural ecological space of the whole province and proposed pathways for reconstructing the natural protected area system.

Results The findings indicated that the natural protected areas in the study region were mainly composed of national parks, nature reserves, and national-level natural reserves. In terms of quantity, scenic spots, forest parks, and wetland parks hold the advantage, aligning aligning spatially with the natural geographic features of the province and exhibiting an overall clustered distribution. Different types of natural protected areas experience significant overlap, with 52 overlapping natural protected areas, accounting for 54.74% of the total number of natural protected areas in the province. Through optimization measures such as new construction, revocation, merging, splitting, and range adjustment, the spatial system was enhanced. Post-optimization, Qinghai Province comprised 82 natural protected areas, covering 41.42% of the total land area, including 80.21% designated as national parks, 15.38% as nature reserves, and 4.42% as nature parks.

Couclusions  This study established a new natural protected area system centered around national parks, supported by nature reserves and various nature parks, effectively ensuring the conservation of crucial ecosystems, biological species, and scenic landmarks across Qinghai Province.