With the aim of assessing differentiation of greenhouse gas emissions as manipulated by plastic film mulching (PFM) from paddy field from a year-round perspective, we determined net ecosystem CO2 exchange (NEE, CO2 flux), CH4 and N2O fluxes from a rice-rapeseed rotation field. PFM and non-mulching (NM) treatments were set from 2014 to 2017 (May 2014 to April 2015, May 2015 to April 2016 and May 2016 to April 2017 were set as Annual 1, Annual 2 and Annual 3, respectively) in Southwest China. Compared with NM, CH4 emissions were increased by 60.00% (P < 0.05), 111.54% (P < 0.05) and 62.07% (P < 0.05) under PFM in Annual 1, 2 and 3, respectively. Additionally, PFM delayed the peaks of CH4 fluxes by 5-10 days during rice season. However, PFM did not affect N2O emissions on the annual basis. PFM reduced the net carbon loss from soil during rice season while had insignificant influence on soil carbon sequestration capacity during fallow and rapeseed seasons. Overall, the mean annual net ecosystem greenhouse gas exchange among three annuals was 32.11% lower under PFM than under NM. Moreover, PFM slightly increased crop yields of both rice and rapeseed. Accordingly, PFM recommended the suitable agricultural management in the rice-rapeseed rotation field for simultaneously alleviating global warming and maintaining crop yields.