A qualitative analysis of in-depth interviews with 92 farmers and 42 policy managers in Wuxi County, the Three Gorges Reservoir Region, was conducted to identify stakeholder preferences for alternative best management practices (BMPs) and to determine the factors that affect their acceptance. Policy manager support for most of the practices was relatively stronger than support by farmers, except for the grade stabilization structure (GSS), hillside ditch (HD) and constructed wetland alternative, owing to their perceptions of soil benefits, economic advantages and environmental advantages. Farmers opposed those practices that occupied cultivated lands or changed the conventional planting methods, such as field border, conservation tillage (CT) and contour buffer strips. They tended to accept the BMPs with off-farm pollution reduction, such as GSS, riparian forest buffer and HD, and the BMPs associated with soil benefits, such as nutrient management and Terrace. The result that almost all respondents did not accept CT differed from reports in the existing literature. There is a significant correlation between the acceptance of some BMPs and the townships where the farmers lived (P ≤ 0.05). The environmental conditions and social factors would affect farmer support for BMPs, including local soil conditions, farming methods, economic income, education level and age. The economic advantages of the BMPs were the main motivation for farmers to accept the practices. Furthermore, intensive education efforts, financial incentives or economic subsidies may promote the adoption of the BMPs in our study area.