Although chemical nitrogen fertilizers have been used worldwide to increase grain yields in the most recent decades , excessive N input may lead to yield loss [20, 39]. Particularly in China, nitrogen fertilizer use has successfully achieved food security in recent decades . However, this high input of N has resulted in serious environmental pollution, which is adverse to the development of sustainable agriculture , e.g., leading to water eutrophication, soil acidification and air pollution [38, 41–43]. Therefore, strategies for the efficient management of N are urgently required. Good et al. identified two ways to increase crop NUE, traditional breeding and transgenic technology . However, cropping techniques are another equally important approach to achieve N efficiency, which can rapidly and further promote the grain yield of highly nutrient-efficient cultivars; for example, intercropping and relay intercropping are resource efficient and environment friendly cropping systems that can increase farm land productivity [20, 31, 45]. In the present study, the NUE was higher in RN than in CN in MM, and in MS, the NUE was significantly higher in RN than in CN. The grain yield of MM increased significantly in CN compared with that in RN, whereas the grain yield of soybean decreased significantly in CN compared with that in RN. The reason for the yield loss might be soil acidification, because multiple fertilizer inputs can result in declines in soil pH , in addition to declines in soil pH that can occur under intercropping soybean with maize . In IMS, the NUE of RN was significantly higher than that of CN, and the maize grain yield was maintained in RN, and soybean grain yield and NUE increased (Tables 1 and 3). These results confirmed that reduced N input led to grain yield loss in MM, in contrast to reduced N supply leading to increased maize yield and NUE in IMS. The results in this study are consistent with those of Yang et al. and Wang et al. who found that relay intercropping can increase resource utilization and land productivity [10, 20] and are also consistent with observations that a reduced N supply can maintain crop yield , whereas excessive N leads to a decline in LER .