<p>Understanding the interactions between land use conflicts (LUC) and ecosystem health (EH) is essential for promoting sustainable human-environment systems, particularly in mountainous regions with pronounced spatial heterogeneity. This study investigates the spatial correlations between LUC and EH in China’s mountainous counties from 2000 to 2020, focusing on variations across major land use transitions and within a three-level stepped terrain pattern. LUC was evaluated using a spatial comprehensive conflict index, EH via an improved vigor-organization-resilience model, and drivers of EH were quantified using the optimal parameters-based geographical detector model. The results indicate that the dominant land use transitions— and thus the primary sources of conflict— occurred between forest and cropland. The most intense conflicts were concentrated in the second step, while EH was highest in the third step. Precipitation and temperature were the main natural drivers of EH, whereas LUC, GDP, population, and the Grain for Green Project were key anthropogenic drivers, with relative importance differing by step. Positive LUC-EH correlations emerged in areas where cropland or grassland shifted to forest, while transitions to cropland often weakened this relationship. Based on these findings, we analyzed the geospatial linkages among land use transitions, LUC, EH, and their driving factors in mountainous regions, and formulated differentiated, step-specific policy recommendations.</p>