Identification of spatial zoning of ecological functions is a prerequisite and fundamental work to support the management of ecological assets in nature reserves. In this study, the spatial and temporal evolution characteristics of land use/cover types, ecosystem service values and landscape ecological risks in the Qilian Mountains National Park Qinghai Area from 1998 to 2018 were analyzed by applying remote sensing, geographic information modeling, landscape ecology and GIS grid methods, and four types of ecological zoning were constructed by Z-score standardization. The results show that:(1) Grassland in Qinghai area of Qilian Mountain National Park was above 55.00%, and the total area transferred between land use types in Qinghai area of Qilian Mountain National Park during 30 years (1998-2018) was 102.49 km², among which the largest area of medium-coverage grassland was transferred out, which was 34.83 km², and the largest area of artificial grassland was transferred in, which was 24.61 km². (2) The ecosystem service value (ESV) of the Qinghai area of Qilian Mountains National Park in three periods (1998, 2008, 2018) was about 27.4 billion yuan/year, and the ecosystem service value per unit area was 1.7294 million yuan/km². The water and wetland ecosystems contributed the largest amount of ecosystem service value, accounting for more than 44.00%, and the alpine river source wetlands and cold temperate coniferous forests were the high value areas of ecosystem service value. (3) The landscape ecological risk index (ERI) of the Qinghai Area of Qilian Mountain National Park in 1998, 2008 and 2018 were 0.2287, 0.2286 and 0.2310, respectively, with an overall good ecological safety status. The landscape ecological risk is dominated by low ecological risk level and lower ecological risk level, accounting for about 90.00%. The landscape ecological risk level of artificial grassland, dry land and construction land is higher. (4) The Qinghai area of the Qilian Mountains National Park was divided into four types of ecological spatial zones:ecologically secure habitat restoration zone (I), ecologically fragile special protection zone (II), ecologically improved development and utilization zone (III), and ecologically preventive conservation and nurturing zone (IV), based on two dimensions of ecosystem service value and landscape ecological risk. The Z-score standardized four-quadrant division results show that the ecological spatial zoning structure of the Qinghai area of the Qilian Mountains National Park shows a trend of steady to good change, according to which a differentiated and targeted ecological spatial zoning control scheme was proposed.