Irrigation mode and straw incorporation play important roles in regulating greenhouse gas emissions and increasing crop yield, which has received extensive attention in agricultural production. In order to clarify the influence of the water management and straw incorporation on the global warming potential(GWP) and crop yield of rice-wheat rotation system, the field experiment was carried out for two years. In the traditional irrigation(TI) and controlled irrigation(CI), on the basis of two modes, they were set to returning wheat straw(WS), biochar returning(BC), no straw returning(NS) three straw management. The rice-wheat rotation system was evaluated for CH_4 and N_2O emission monitoring and crop yield. It provided the scientific basis for the sustainable development of agriculture by selecting the optimal water management and straw returning combination. The results showed that compared with NS treatment, the annual CH_4 emission of WS and BC increased by 106.02% and 36.77%, respectively, while the average annual N_2O emission decreased by 27.25% and 16.21%, respectively. The average yield of rice was increased by 6.49% and 5.90%, respectively, and the annual GWP_(yield-scaled) increased by 40.53% and 8.07%, respectively. In the whole rotation cycle, the CH_4 emission of CI system decreased by 79.63% compared with TI, and N_2O emission increased by 27.03%, the average yield of rice was increased by 0.42%, and the GWP_(yield-scaled) decreased by 60.32%. Controlled irrigation with biochar(CIB) had the lowest GWP_(yield-scaled), which was 53.81%, 70.49%, 59.77%, 4.46%, 11.92% lower than traditional irrigation with no straw returning(TINS), traditional irrigation with wheat straw(TIS), traditional irrigation with biochar(TIB), controlled irrigation with no straw returning(CINS), and controlled irrigation with wheat straw(CIS), respectively. Significant interactions between irrigation mode and straw management practices were found on annual greenhouse gas emissions, but not on crop yields. It can be seen that controlled irrigation withbiochar may reduce greenhouse gas emissions while increase crop yield in rice-wheat cropping areas.