Nitrate accumulation at depth in variable charge soils in humid tropics and subtropics affects nitrogen (N) leaching to groundwater. However, the mechanisms on the nitrate accumulation in relation to regolith (soil and saprolite) properties are poorly understood. In this study, four upland regoliths were selected in a typical red soil Critical Zone of humid subtropical China. These regoliths with a thickness of 6–8 m, which developed from Quaternary red clay underlain by sandstone bedrock, were acidic, highly weathered, and clay loam to clay in texture. We analyzed the relationships between nitrate concentrations and the regolith physiochemical properties. The results showed that regolith pH was negatively correlated with nitrate concentrations, whereas crystalline iron (Fe) and aluminum (Al) and anion exchange capacity (AEC) were positively correlated with nitrate concentrations at depths below both soil surface and 1 m. Bulk density (BD) was significantly related to nitrate concentrations only at depths below soil surface, while depth, clay, amorphous Fe and Al, total organic carbon (C), and total N were significantly related to nitrate concentrations only at depths below 1 m. There was no significant correlation between nitrate concentrations and sand, silt, silicate bound Fe or Al, C/N, or moisture at depths below both soil surface and 1 m. Based on the random forest analysis, the relative contributions of pH, crystalline Fe, depth, AEC, BD, crystalline Al and amorphous Fe to explaining nitrate concentration variations were 28.3%, 9.5%, 4.3%, 3.4%, 2.9%, 2.8% and 2.6%, respectively. The concentration of crystalline Fe was ten times that of crystalline Al, which would account for its larger contribution to the nitrate variations. Nitrate accumulation at depth was most likely controlled both by electrostatic adsorption on crystalline Fe and Al oxides and low hydraulic conductivity of the regolith at depth, which appeared to be largely influenced by regolith pH and competitive anions. Our findings shed light on regolith internal property controls on nitrate legacy in the subtropical vadose zone and may help control nitrate contamination of groundwater in intensified agricultural regions.