Abstract: Scientific understanding of the trade-offs between services is crucial for the scientific management and protection of ecosystems and the formulation of resource management policies. This study integrated meteorological, land use, and soil data to assess the ecosystem services, namely, water yield (WY), soil erosion (SE), and carbon sinks (CS), in peak-cluster depression basins on the Sino-Vietnamese border in China during 2000–2020. It analyzed the trade-offs and synergistic relationships among the three ecosystem services and their time-lag effects and driving mechanisms with the help of pixel-by-pixel time-lag intercorrelation and geographical detector methods. Results show that: 1) from 2000 to 2020, the key ecosystem service indicators in the peak-cluster depression basins on the Sino-Vietnamese border in China demonstrated a significant and synergistic trend of positive change. The WY increased at a rate of 11.99 mm/yr, CS increased at a rate of 2.44 g C/(m²∙yr), and SE decreased at a rate of 0.06 t/(ha∙yr). 2) Most areas showed a synergistic relationship across the three ecosystem services, and the areas with a trade-off relationship were mostly concentrated in Baise City and the southwest of Chongzuo City, Guangxi. 3) The time-lag effect between SE and WY was mostly concentrated in 0 yr, that between SE and CS was mostly concentrated in 5 yr, and that between CS and WY was mostly concentrated in 1 yr. 4) Population density was the controlling factor between SE and WY. Vegetation coverage factor is the main controlling factor between SE and CS. The lithologic factor is the main controlling factor between CS and WY. Studying the trade-off relationship of ecosystem services at spatial and temporal scales on the Sino-Vietnamese border in China karst areas can provide a basis for regional ecological construction and development strategies, and it is conducive to meeting regional interest needs, maximizing comprehensive benefits, balancing the ecological environment, and achieving regional sustainable development.