The investigation into the impact of the Three Gorges Project on ecosystem services is crucial for ecological conservation, sustainable developmen and ecological management decisions. While numerous studies have focused on assessing the current state of regional ecosystem services, there remains a gap in research related to simulating the spatiotemporal changes and impact pathways. The objective of this paper is to uncover the direct and indirect impact pathways of ecosystem service value (ESV) in the reservoir area altered by the construction of the Three Gorges Dam project, by using the structural equation model (SEM) method. Additionally, this study aims to identify spatial and temporal changes in ecosystem service relationships over the 30 years before and after the dam's construction, utilizing self-organizing maps (SOM). The results of the study reveal that land use and land cover (LULC) factors predominantly exert direct negative effects on ESV. In comparison, socioeconomic development (ECO) and meteorological development (MET) factors have a nuanced impact on ESV, with MET factors exhibiting the strongest positive effect on ESV through the pathway MET → LULC → ESV. Furthermore, the application of SOM indicates that between 1990 and 2020, the patterns of ecosystem service bundles were spatially heterogeneous. Additionally, trade-offs and synergies between ecosystem service bundles are relevant to hydrological regulation services. These findings contribute to a comprehensive understanding of how various factors interact and influence ESV through multiple pathways. The intricate relationships among ecosystem services highlighted in the study are valuable for guiding ecological management at various scales.