Against the backdrop of rapid urbanization, the spatial relationship between natural ecosystem services (NES) and cultural ecosystem services (CES) has become a focal issue for regional sustainable development, while the mechanisms underlying their trade-offs and synergies require urgent clarification. Using Jiangxi Province as a case study, this research integrated multi-source data to analyze the spatial association patterns and driving mechanisms of NES and CES, and explored how these relationships could inform pathways for regional spatial governance. Specifically, the spatial distribution pattern of CES was mapped using the SolVES model. Structural equation modeling was then used to characterize the pathways through which residents’ perceptions influenced CES. Additionally, the Transformer-GeoShapley model was applied to identify and quantify the association patterns between NES and CES, thereby addressing the limitations of previous studies in interpreting their coupling mechanisms. Building on this, a research framework of “ecological supply-social empowerment-collaborative governance” was developed. By explicitly embedding the identified nonlinear interactions among ecosystem services into territorial spatial planning scenarios, this framework facilitated the transition from quantitative assessment to governance practice. The results showed that CES in Jiangxi Province exhibited a spatial pattern of “moderately high in the central region and relatively low around the periphery.” High-value areas for recreational opportunities, aesthetic landscapes, and related cultural services were concentrated in Nanchang, Jiujiang, and other zones where favorable natural conditions overlapped with rich cultural-historical endowments. In contrast, NES displayed a pattern of “high at the edges and low in the center,” reflecting their strong dependence on natural background conditions. Residents’ perceptions of CES were structured around a dual core of natural environmental experience and cultural-historical cognition, with long-established ethnic groups showing higher identification with and attachment to local cultural heritage. Moreover, synergistic relationships between NES and CES were mainly distributed in eco-cultural composite areas, especially around northern Poyang Lake, while trade-off relationships were concentrated in the agriculture-dominated southern regions. The study suggested that this spatial differentiation could be dynamically balanced through zonal regulation, landscape pattern optimization, and targeted cultural heritage conservation and utilization measures. Overall, the findings not only provided a new paradigm for elucidating the coupling mechanisms of the “nature-culture” system in Jiangxi Province, but also proposed a Chinese approach that could be referenced by similar regions worldwide in coordinating ecological conservation with cultural heritage transmission.