The Three Gorges Reservoir Region (TGRR) in China is an ecologically and politically important region experiencing rapid land use/cover changes and prone to many environment hazards related to soil erosion. In the present study, we: (1) estimated recent changes in the risk pattern of soil erosion in the TGRR, (2) analysed how the changes in soil erosion risks could be associated with land use and land cover change, and (3) examined whether the interactions between urbanisation and natural resource management practices may exert impacts on the risks. Our results indicated a declining trend of soil erosion risk from 14.7 × 10⁶ t in 2000 to 1.10 × 10⁶ t in 2015, with the most risky areas being in the central and north TGRR. Increase in the water surface of the Yangtze River (by 61.8%, as a consequence of water level rise following the construction of the Three Gorges Dam), was found to be negatively associated with soil erosion risk. Afforestation (with measured increase in forest extent by 690 km² and improvement of NDVI by 8.2%) in the TGRR was associated with positive soil erosion risk mitigation. An interaction between urbanisation (urban extant increased by 300 km²) and vegetation diversification (decreased by 0.01) was identified, through which the effect of vegetation diversification on soil erosion risk was negative in areas having lower urbanisation rates only. Our results highlight the importance of prioritising cross-sectoral policies on soil conservation to balance the trade-offs between urbanisation and natural resource management.