Natural changes and human disturbance have far-reaching influences on ecosystem services (ESs) in arid alpine basins. In this paper, the Issyk-Kul Basin (IKB) is taken as a case study to systematically quantify 5 ES distributions and determine ES hotspots/coldspots. We used Spearman correlation analysis to explore trade-offs and synergies between ESs. Then, ES bundles and socioecological drivers of ESs were identified by utilizing K-means clustering and redundancy analysis (RDA). The results revealed that the water yield (WY) and soil retention (SR) in the IKB increased significantly from 1992 to 2015, but food production (FP) and habitat quality (HQ) exhibited decreasing trends. Correlation analysis indicated a synergistic relationship between SR and WY/NPP (R = 0.34/R = 0.68; p < 0.001), and a trade-off relationship between FP and HQ (r = −0.35; p < 0.01). Based on cluster analysis, three ES bundles were identified, including the “Agriculture bundle”, “Soil & vegetation bundle” and “Habit quality bundle”. Redundancy analysis (RDA) indicated that WY and SR were mainly affected by natural factors (i.e., precipitation, slope and vegetation coverage), while FP and HQ were more sensitive to human factors (i.e., population density, percentage of cropland and percentage of urban). Our findings promote a better understanding of the complex relationship between ESs, and provide a reference for developing win-win management strategies for socioeconomic development and ecological protection in alpine basins.