Climate warming is anticipated to change the terrestrial carbon/nitrogen cycle through its impact on the fluxes of greenhouse gases such as CO2 and N2O. This study investigated the effect of diurnal warming and acid rain on CO2 and N2O emissions from soil-plant systems in a winter wheat–soybean rotation cropland. Field rotational experiments of winter wheat and soybean were conducted by simulating diurnal warming and acid rain. Manipulated experiments included the control (CK), diurnal warming (T, + 2 °C), acid rain (AR, pH = 2.5), and the combined treatment (TAR, + 2 °C and acid rain). CO2 and N2O fluxes from soil-plant systems were measured using a static chamber-gas technique. The results showed that in the winter wheat and soybean growing seasons, compared with CK treatment, T, AR, and TAR treatments did not change the accumulative amount of CO2 emission (AAC) across the full growth period (p ˃ 0.05), although T treatment significantly increased soil AAC (p < 0.05) at the grain filling-maturity stage. On the contrary, T and AR treatments significantly increased the accumulative amount of N2O emission (AAN) in winter wheat and soybean croplands (p < 0.05), which was attributed to leaf nitrate reductase activity, total biomass, and soil NO3−–N content. In addition, there was a significant interaction between warming and acid rain on N2O flux. The AAN from the winter wheat cropland under treatments was in the order: TAR ˃ AR ˃ T ˃ CK. Our findings suggest that diurnal warming and acid rain had no significant effect on CO2 emissions from soil-plant systems, but significantly increase N2O emissions in winter wheat and soybean growing seasons. Moreover, diurnal warming would strengthen the positive effect of acid rain on N2O emissions from soil-plant systems in winter wheat farmland.