The effects of maize straw return and N fertilizer application on soil quality and crop yield have been extensively investigated. However, the effects of different amounts of maize straw returned to the field with different nitrogen application rates on the soil–crop system quality, abundance of functional N cycle microorganisms, N2O emissions, and crop N nutrition status of crops have not been thoroughly explored. The objective of this study was to assess the effects of different summer maize straw return rates and N application rates on i) soil quality and crop productivity; ii) the community of N cycle functional microorganisms and N2O emission; and iii) crop N status. The results indicated that crop yields increased by 7.62 to 12.69% at 210 kg ha–1 of N application for full straw return (SN) and half return (1/2SN) compared to the no-return treatment (CK). No significant difference was noted in the yields between the full straw return reduced by 15% (178.5 kg N ha–1) of N fertilizer (S-15%N) and SN. The surface soil layer (0–20 cm) showed significantly higher levels of soil organic matter (SOM), the community of N-cycling functional microorganisms, crop N nutrition status and N uptake efficiency in SN, 1/2SN, and S-15%N as compared to other treatments. Compared to SN, S-15%N and 1/2SN reduced cumulative N2O emission fluxes by 19.11 and 5.51%, respectively. Furthermore, the nitrogen nutrient index (NNI) values of 1/2SN and S-15%N were closer to the critical N requirement than SN. In summary, schemes for determining the optimal rates of straw return and N application (1/2SN and S-15%N) based on SOM, NNI, cumulative N2O emission fluxes, and yield can be applied to the annual production of winter wheat and summer maize in China.