Efficient and fast methods for disposing rapeseed straw are badly needed in the rice-rapeseed rotation system, where rice is planted immediately after the rapeseed harvest. In this research, the effects of rapeseed straw returning (6 g kg–1) on rice cultivation soil organic carbon accumulation, CH4 and CO2 emissions, and total organic carbon (TOC) contents of the aqueous layer in the flooded condition within the 60 days of incubation experiment were studied. The experimental results showed that the straw addition increased the peak of CH4 and CO2 emission flux by 32.9% and 6.3%, respectively, compared to that of without straw. The CO2 emissions were mainly concentrated during the first 1–10 days, while CH4 emissions were concentrated during the latter 30–60 days. The organic carbon contents in soil of straw addition varied from 21.5 to 23.1 g kg–1 compared with that in the range of 20.7–22.3 g kg–1 without straw. With straw addition, the TOC contents in aqueous layer were increased continuously from 55.1 to 68.1 mg L–1 during the late periods (30–60 days). The experimental results of this study indicated that an increase of external carbon addition by using rapeseed straw in the soil will have a better cultivation environment for rice crops and very possibly result in a higher amount of harvest. Therefore, the straw addition in the soil will be more environmental friendly and have economic benefit in the rice-rapeseed rotation system.