Significant heterogeneity has been observed among different ecosystem services (ES). Understanding the trade-offs and synergies among ES and delineating ecological functional zones is crucial for formulating regional management policies that improve human well-being and sustainably develop and maintain ecosystems. In this study, we used the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) and Carnegie–Ames–Stanford Approach (CASA) models to evaluate the spatial distribution patterns of nine ES (food supply, raw material supply, water resource supply, water connotation, climate regulation, soil conservation, water purification, habitat quality, and entertainment tourism) in the Qilian Mountains from 2000 to 2018. We also investigated the trade-offs and synergistic relationships among ES through Spearman correlation analysis, identified ES hotspots through exploratory spatial data analysis, and identified ES bundles (ESB) using K-means clustering. Our results revealed that water purification and habitat quality remained relatively stable, while food supply, raw material supply, water resource supply, water conservation, climate regulation, soil conservation, and entertainment tourism increased by 1038.83 Yuan·ha−1, 448.21 Yuan·ha−1, 55.45 mm, 7.80 mm, 0.60 tc·ha−1, 40.01 t·ha−1 and 4.82, respectively. High-value areas for water resource supply were mainly concentrated in the high-altitude mountainous area, whereas high-value areas for soil conservation were found in the western and eastern parts of the study area. The low-value areas of water purification were primarily located in the east, while the remaining six services were highly distributed in the east and were less common in the west. Correlation analysis showed that water resource supply, water conservation, and soil conservation exhibited a synergistic relationship in the Qilian Mountains. Moreover, food supply, raw material supply, climate regulation, habitat quality, and entertainment tourism showed synergistic relationships. However, there were trade-offs between food supply and water purification as well as water resource supply, and habitat quality showed a tradeoff with water resource supply, water conservation, and soil conservation. We identified four ESB. The food supply bundle consisted mainly of farmland ecosystems, while the windbreak and sand fixation and ecological coordination bundles were dominant in the Qilian Mountains. Notably, the area of the water conservation bundle increased significantly. Our comprehensive findings on ES and ESB can provide a theoretical foundation for the formulation of ecological management policies and the sustainable development of ecosystems in the Qilian Mountains.