Contemporary agriculture is shifting from a single-goal to a multi-goal strategy, which in turn requires choosing best management practice (BMP) based on an assessment of the biogeochemical effects of management alternatives. The bottleneck is the capacity of predicting the simultaneous effects of different management practice scenarios on multiple goals and choosing BMP among scenarios. The denitrification-decomposition (DNDC) model may provide an opportunity to solve this problem. We validated the DNDC model (version 95) using the observations of soil moisture and temperature, crop yields, aboveground biomass and fluxes of net ecosystem exchange of carbon dioxide, methane, nitrous oxide (N2O), nitric oxide (NO) and ammonia (NH3) from a wheat-maize cropping site in northern China. The model performed well for these variables. Then we used this model to simulate the effects of management practices on the goal variables of crop yields, NO emission, nitrate leaching, NH3 volatilization and net emission of greenhouse gases in the ecosystem (NEGE). Results showed that no-till and straw-incorporated practices had beneficial effects on crop yields and NEGE. Use of nitrification inhibitors decreased nitrate leaching and N2O and NO emissions, but they significantly increased NH3 volatilization. Irrigation based on crop demand significantly increased crop yield and decreased nitrate leaching and NH3 volatilization. Crop yields were hardly decreased if nitrogen dose was reduced by 15% or irrigation water amount was reduced by 25 %. Two methods were used to identify BMP and resulted in the same BMP, which adopted the current crop cultivar, field operation schedules and full straw incorporation and applied nitrogen and irrigation water at 15 and 25% lower rates, respectively, than the current use. Our study indicates that the DNDC model can be used as a tool to assess biogeochemical effects of management alternatives and identify BMP.