Optimizing long-term best management practices (BMPs) is of vital importance for water quality management, especially for nonpoint source (NPS) pollution. However, changes in the efficiency of BMPs over time have not been incorporated and a proper method for determining long-term BMP configuration strategies is still lacking. In this study, the long-term BMP optimization method (LBMP-OM) was developed for recommending the BMP maintenance-replacement strategies and optimizing the BMP configuration. This new method was then tested in the Daning Watershed, Three Gorges Reservoir Region, China. Based on the results, a 1-year maintenance period and a 3-year replacement period was recommended for a filter strip by considering a changing BMP effectiveness rather than a constant effectiveness and by discussing the rationality of experts' suggestions for maintenance and replacement strategies regarding the regulation of NPS pollution. At the watershed scale, the total cost dropped by 57.36% by introducing the LBMP-OM method compare to the original method. This new method extended the long-term management and configuration of BMPs. Display omitted •A new method was proposed for the optimization of BMPs at watershed scale.•Changes in future BMPs efficiency were qualitied.•Dynamic efficiency and cost were incorporated instead of static assumption.•Optimal maintenance and replacement were provided for filter strip.•Cost dropped by 57.36% if the new method was used for BMP configuration.