A field experiment was conducted in the Key Field Station for Monitoring of Eco-Environment of Purple Soil of the Ministry of Agriculture of China in the farm of Southwest University in Chongqing. Static opaque chamber and gas chromatography methods were used to study the effect of plastic film mulching on CH4 and N2O emissions characteristics from a rice-rapeseed crop rotation in situ for one year. The results showed that CH4 and N2O emissions are mainly concentrated in the early stages of the growth of each crop and there is a clear seasonal variation of CH4 emissions during the rice growing period and N2O in the rapeseed growing period. The CH4 flux changed from -0.45 to 1.90 mg·(m2·h)-1 and the N2O flux varied between -46.1 and 2040.7 μg·(m2·h)-1 over the entire year. Plastic film mulching was found to increase the total emissions of CH4 and N2 O, with the total CH4 emission of(27.22±4.48) kg·hm-2 over the entire year, which is 26.22% higher than that of the non-mulching treatment(19.93±0.56) kg·hm-2. The total amount of N2O emissions under film mulching treatment increased 16.6% from (11.27±2.77) kg·hm-2 under no mulching treatment to (13.14±0.82) kg·hm-2. The results analyzed for soil moisture and soil temperature showed that mulching significantly increased the soil moisture during the rapeseed season, while there was no obvious correlation with soil temperature (at depths of 5 cm and for the surface temperature) for each crop season. During the rapeseed growing season, CH4 and N2O emissions negatively correlated with soil moisture and has a significant negative correlation during the seedling period with film mulching treatment. Moreover, under the two treatments, the correlation between CH4 and N2O emissions and soil temperature was negligible. This study indicates that plastic film mulching impacts CH4 and N2O emissions at different growth stages of the crops, which changes the proportion of the emission of the two gases over the whole growth period, and promotes the emission of CH4 and N2O in the rice-rapeseed system. In the time scale of 100 years, the integrated global warming potentials (GWP) of CH4 and N2O emission under plastic film was a CO2 equivalent of 4213.00 kg·hm-2 compared with that under conventional treatment of 3454.17 kg·hm-2. Conventional emits 22.0% less CO2, indicating that plastic film mulching is not an effective measure for carbon sequestration.