A comprehensive understanding of the trade-off/synergy relationships that exist among multiple ecosystem services (ESs) has become increasingly important for ecological management and sustainable development. However, the determination of the factors that promote trade-off/synergy relationships and the extent to which the driving factors affect these complex relationships have not been well studied, limiting the effectiveness of sustainable ecosystem management. This study employed the Yangtze River Delta region in China as the study area and investigated the spatiotemporal changes in three ESs, namely, carbon storage (CS), water purification (WP), and habitat quality (HQ), from 2005 to 2015. A trade-off/synergy degree (TSD) indicator was developed that allowed for the quantification of the trade-off/synergy intensity, and the spatial pattern of the TSD between ESs in the YRD region was analyzed. Furthermore, a geographically weighted regression (GWR) model was used to analyze the relationship between the driving factors and trade-offs/synergies. The results revealed that CS, WP, and HQ decreased by 1.17%, 2.49%, and 3.38%, respectively. The TSD indicator showed that the trade-off/synergy relationships and their magnitudes were spatially heterogeneous. The coefficients of the natural and socioeconomic factors obtained from the GWR indicated that their impacts on the trade-offs/synergies vary spatiotemporally. The impact factors had both positive and negative effects on the trade-offs/synergies. The values of R2 and AIC implied that the selected factors had significant explanatory power for the trade-off/synergy relationships between paired ESs. The findings could improve the understanding of the spatiotemporal dynamics of trade-offs/synergies and their spatially heterogeneous correlations with related factors.