Understanding the spatiotemporal characteristics of trade-offs and synergies among multiple ecosystem services (ESs) is the basis of sustainable ecosystem management. The ecological environment of valley basins is very fragile, while bearing the enormous pressure of economic development and population growth, which has damaged the balance of the ecosystem structure and ecosystem services. In this study, we selected two typical valley basins—Guanzhong Basin and Hanzhong Basin—as study areas. The spatial heterogeneity of trade-offs and synergies among multiple ESs (net primary production (NPP), habitat quality (HQ), soil conservation (SC), water conservation (WC), and food supply (FS)) were quantified using the correlation analysis and spatial overlay based on the gird scale to quantitatively analyze and compare the interaction among ESs in two basins. Our results found that: (1) Trade-offs between FS and other four services NPP, HQ, SC, and WC were discovered in two basins, and there were synergistic relationships between NPP, HQ, SC, and WC. (2) From 2000 to 2018, the conflicted relationships between paired ESs gradually increased, and the synergistic relationship became weaker. Furthermore, the rate of change in Guanzhong Basin was stronger than that in Hanzhong Basin. (3) The spatial synergies and trade-offs between NPP and HQ, WC and NPP, FS and HQ, SC and FS were widespread in two basins. The strong trade-offs between pair ESs were widly distributed in the central and southwest of Guanzhong Basin and the southeast of Hanzhong Basin. (4) Multiple ecosystem service interactions were concentrated in the north of Qinling Mountain, the central of Guanzhong Basins, and the east of Hanzhong Basin. Our research highlights the importance of taking spatial perspective and accounting for multiple ecosystem service interactions, and provide a reliable basis for achieving ecological sustainable development of the valley basin.