The optimization of best management practices (BMPs) at the watershed scale is notably complex because of the social nature of decision process, which incorporates information that reflects the preferences of decision makers. In this study, a preference-based multi-objective model was designed by modifying the commonly-used Non-dominated Sorting Genetic Algorithm (NSGA-II). The reference points, achievement scalarizing functions and an indicator-based optimization principle were integrated for searching a set of preferred Pareto-optimality solutions. Pareto preference ordering was also used for reducing objective numbers in the final decision-making process. This proposed model was then tested in a typical watershed in the Three Gorges Region, China. The results indicated that more desirable solutions were generated, which reduced the burden of decision effort of watershed managers. Compare to traditional Genetic Algorithm (GA), those preferred solutions were concentrated in a narrow region close to the projection point instead of the entire Pareto-front. Based on Pareto preference ordering, the solutions with the best objective function-values were often the-more desirable solutions (i.e., the minimum cost solution and the minimum pollutant load solution). In the authors' view, this new model provides a useful tool for optimizing BMPs at watershed scale and is therefore of great benefit to watershed managers.