Ecosystem services are directly related to human well-being. Previous studies showed that management policies and human activities alter the trade-offs and synergies of ecosystem services. Taking effective measures to manage the trade-offs and synergies of ecosystem services is essential to sustain ecological security and achieve a “win-win” situation between society and ecosystems. This study investigated the spatiotemporal changes of water yield, soil conservation, and carbon sequestration in the Jiulianshan National Nature Reserve from 2000 to 2020 based on the InVEST model. We distinguished spatial patterns of trade-offs and synergies between ecosystem services using the correlation relationship analysis. Then we analyzed the response of ecosystem services relationships among different vegetation types and elevation bands. The results showed that water yield and carbon sequestration presented an overall upward trend, while soil conservation remained a marginal degradation. Rising ecosystem services were mainly in the central, western, and southeastern regions, and declining areas were mainly distributed in the midwestern and northeastern fringes. Synergies spatially dominated the interactions among water yield, soil conservation, and carbon sequestration, and the trade-offs were primarily concentrated in the northern, southern, and southwestern fringes. Among the different vegetation types, synergies dominated ecosystem services in broad-leaved forests, coniferous forests, mixed forests, and Moso bamboo forests and in the grass. The trade-offs were gradually reduced with elevation. This study highlighted that trade-off of ecosystem services should be incorporated into ecological management policies, strengthening the effectiveness of nature reserves in protecting and improving China’s ecosystem services.