Soil organic carbon (SOC) dynamics significantly influence ecosystem carbon source-sink balance, particularly in agroecosystems. However, uncertainty remains regarding optimal land use types for maximizing farmland carbon storage across different soil types, and identifying effective land management practices for enhanced carbon accumulation is essential for reducing agricultural emissions and strengthening carbon sinks. This study examined SOC variations in eastern Yunnan's subtropical highlands (2,132 sites), analyzing topsoil (0-20 cm) across five land uses (dryland, irrigated land, forestland, grassland and plantation) of five soil types (red, yellow, yellow-brown, brown, purple). The investigation explored relationships between SOC and edaphic factors (26 elements) to determine SOC influencing factors. The study area demonstrated a mean SOC content of 27.78 g kg-1, with distinct spatial heterogeneity characterized by lower values in the southwestern sector and higher concentrations in the northeastern region. Brown soils displayed the highest SOC content (P<0.05), followed by yellow-brown then red, yellow, and purple soils. Irrigation significantly enhanced SOC storage, particularly in brown soils where irrigated land contained 2.2-, 2.4-, and 1.6-times higher SOC than forestland, grassland, and dryland, respectively. Similar irrigation benefits occurred in purple, yellow, and yellow-brown soils, indicating moisture limitation as the primary SOC constraint. Notably, SOC exhibited strong positive correlations with nitrogen, sulfur, and selenium. Nitrogen fertilization demonstrated dual benefits: enhancing SOC sequestration and promoting Se enrichment in crops, potentially supporting specialty agriculture. Although land use impacts on SOC varied across soil types (P>0.05), irrigation consistently emerged as the optimal management for carbon sink enhancement. These findings suggest that targeted water management could effectively reduce farmland carbon emissions in moisture-limited subtropical highlands. Strategic nitrogen application offers co-benefits for soil fertility and selenium biofortification, providing practical pathways for climate-smart agriculture in similar ecoregions.