Most studies on the ecosystem service value (ESV) only focus on spatial/temporal heterogeneity or single driving effects, but little is known about the combined effects of nature-human activity-policy on ESV in the fragile karst areas. This study aimed to investigate the spatial-temporal heterogeneity of ESV between 1990 and 2020 in a representative karst trough valley in SW China. The dynamic degree of land use, the land-use transfer matrix, sensitive analyses, Geo-Detector, and Hot- and cold-spots analyses were used to determine the interactions between ESV and the natural, human activity, and policy-driving factors. The results showed that from 1990 to 2020, forestland accounted for more than 62.32% of the total area, and construction land increased continuously as a result of urbanization. The conversion from forestland to cropland dominated the land-use transfer. The ESV decreased sharply between 1990 and 2000 and slowly increased from 2000 to 2020, causing a total reduction of 562.91 million yuan in ESV, due largely to the occupation of forestland and grassland by cropland. Soil type (8.00%) had the largest explanation rate for the spatial-temporal heterogeneity of ESV, followed by population density (7.71%) and altitude (6.34%). Policy factors not only markedly influenced the ecosystem structure and function and tradeoff and synergy but also regulated their interactions with other driving factors. Our results have great significance for understanding the interaction effect of natural sources and human activities on changes in ESV in karst areas.