A deeper understanding of the effects of experimental warming and elevated ozone (O3) concentration on carbon dioxide (CO2) fluxes is imperative for reducing potential CO2 emissions in agroecosystems, but are less understood particularly in rotational wheat (Triticum aestivum)—soybean (Glycine max) croplands. In order to understand such effects on CO2 fluxes from winter wheat-soybean rotation, a field experiment was conducted by using the open-top chamber (OTCs) during the growing seasons of 2012 and 2013 at an agro-ecological station in southeast China. The experimental treatments included the control (CK), experimental warming (T, crop canopy temperature increased by ~2 °C), elevated O3 concentration (O, O3 concentration about 100 ppb) along with temperature enhancement (OT, elevated ~2 °C temperature plus 100 ppb O3). The results showed that warming significantly increased the mean CO2 fluxes (MCF) and the cumulative amount of CO2 (CAC) from soil and soil-crop systems, while elevated O3 and warming enhancement (OT) significantly reduced MCF and CAC. Besides, warming significantly reduced the biomass of winter-wheat, but it insignificantly decreased the biomass of soybean in the harvest period. The O and OT treatments significantly reduced the biomass of winter-wheat and soybean cropping systems in the harvest time. Both warming and elevated O3 concentration decreased the temperature sensitivity coefficients (Q10) in soil respiration during the experimental period. Overall, our results indicate that elevated O3 concentration compensates the effect of warming on CO2 emission to some extents, which has a positive feedback impact on the climate system.