The effects of nighttime warming and rainfall increasing on crop productivity and soil greenhouse gas emissions are few studied. This study was conducted with a field experiment to investigate the effects of nighttime warming, rainfall increasing and their interaction on wheat grain yield, methane (CH4) and nitrous oxide (N2O) emissions during a winter wheat growing season in the North China Plain (NCP). The results showed that nighttime warming and rainfall increasing significantly altered soil temperature and moisture, and thus the CH4 and N2O emissions from the soil. Nighttime warming significantly promoted soil CH4 uptake by 21.2% and increased soil N2O emissions by 22.4%. Rainfall increasing stimulated soil N2O emissions by 15.7% but decreased soil CH4 uptake by 18.6%. Nighttime warming significantly decreased wheat yield by 5.5%, while rainfall increasing enhanced wheat yield by 4.0%. The results indicate that the positive effect of nighttime warming on CH4 uptake and negative effect on wheat yield can be offset by rainfall increasing in the NCP. Generally, rainfall increasing significantly raised the global warming potential and greenhouse gas intensity induced by CH4 and N2O emissions. Overall, this study improves our understanding of agroecosystem C and N cycling in response to nighttime warming and rainfall increasing under future climate change.