To increase crop productivity while reducing environmental costs, an integrated soil–crop system management (ISSM) strategy was developed and successfully adopted in China. However, little information is available on the long-term ISSM effects on maize agronomic and environmental performance. Therefore, we evaluated the effects of ISSM with combining inorganic and organic fertilizers on maize productivity, N use efficiency (NUE) and N balance and losses as compared with farmers’ practice (FP) and high-yielding practice (HY), based on an 11-year field experiment in Northeast China. Maize yield in ISSM (11.7–14.3 Mg ha−1) achieved 97.7% of that in HY and was increased by 27% relative to FP. The excellent yield performance in ISSM was mainly attributed to optimum plant population structure and yield components. Annual N surplus in ISSM was only 7 kg ha−1, which was considerably lower than that in FP (52 kg ha−1) and HY (109 kg ha−1). Consequently, ISSM obtained significantly lower N losses and greenhouse gases emissions and higher NUE. In contrast to FP, crop performance in ISSM showing better sustainability and inter-annual stability. In conclusion, ISSM is an effective strategy to achieve long-term sustainable high crop yields and NUE with less environmental costs in the intensive agricultural system.