‘High input, high output’ intensive agriculture in China has contributed greatly to food security, but caused heavy agricultural nitrogen (N) losses. Modern Agriculture faces the dual challenges of increasing food supply and protecting the environment for sustainable agriculture. In order to reduce N losses in rice production systems, two field experiments at different N levels (Exp. I) and integrated crop management practices (Exp. II) were conducted. The results indicated that the newly bred ‘super’ rice varieties have great yield potentials, but this can only be realized at very high N rates with low N efficiency, and large amounts of N residue in the soil. However, by adopting multiple crop management practices, including increasing the crop density, optimizing the amount and ratio of N applications, using an alternate wetting and soil drying irrigation pattern, adding organic fertilizer, and increasing tillage depth, soil structure, soil enzymatic activities, and root activities were significantly improved. The improved soil fertility and root activities contributed greatly to the nutrient uptake ability of crops, and decreased N residues in the soil. With multiple crop management practices, the N fertilizer input was reduced by 10 %, the fertilizer N recovery efficiency was increased by 40.7 %, and N losses to the environment were decreased by 47.8 %, compared with local farmers’ practices. Considering the urgency of reducing the adverse environmental risks of N losses and pollution from rice production without sacrificing rice yield, multiple crop management practices should be adopted in rice production, especially at high crop yield levels with large N inputs.