Methane (CH₄) is one of the most important greenhouse gases and plays an important role in atmospheric chemistry. Rice fields have been identified as an important source of atmospheric CH₄. Because permanently flooded paddy fields create the most favorable situation for CH₄ production and emit CH₄ all year round, they are thought to contribute the greatest amounts of CH₄. Draining the permanently flooded paddy fields in the fallow season is supposed to be a good option for mitigating CH₄ emission. However, those paddy fields distributed in the hilly area of southwest China face the problem of water shortage. This means that transplanting rice in the following year would be hindered, if the fields were drained in the previous fallow season. In recent years, a new technology involving improved plastic film mulching for rice cultivation has been developed. It is an alternative to permanently flooded rice cultivation technology, which promises to save water, and in addition, would allow drainage in the fallow season without impeding the next rice transplanting session. The effects of water management in winter and of plastic film mulching during rice cultivation on CH₄ emission throughout the year were explored using winter paddy fields in the hilly region of Central Sichuan. A field experiment was carried out using the static chamber-gas chromatograph method to monitor CH₄ emissions in the paddy fields. Three treatments were designed: Treatment CF (continuous flooding all year round), Treatment TF (drained in winter and flooded during the rice growing season), and Treatment PM (drained and mulched in winter and mulched during the rice growing season). The results showed that methane emission for Treatments CF, TF, and PM was 16.1 g/m², 1.4 g/m², and 2.7 g/m², respectively, during the winter fallow season and 57.7 g/m², 27.7 g/m², and 13.5 g/m², respectively, during the rice-growing season. Compared with Treatment CF, Treatments TF and PM reduced the annual CH₄ emission by 60.6% and 78.0%, respectively, and lowered the CH₄ flux peak during the rice-growing season by 33.0% and 56.1%, respectively. During the fallow season, in Treatments TF and PM, CH₄ emission from ridge and ditch areas was significantly correlated with soil temperature (P < 0.05), but negatively with soil redox potential (soil Eh) (P < 0.05). However, CH₄ emission was positively correlated with soil temperature in Treatment CF (P < 0.05). During the rice-growing season, in Treatment CF, CH₄ emission was significantly and positively related to soil temperature (P < 0.05), and negatively to soil Eh (P < 0.05). In Treatment TF, CH₄ emission was only negatively related to soil Eh (P < 0.05), and in Treatment PM, CH₄ emission from the ditches was significantly and positively related to soil Eh (P < 0.05). The soil dissolved organic carbon (DOC) and soil microbial biomass carbon (MBC) contents were much higher during the rice-growing season than during the fallow season (P < 0.05). The findings may provide important data and a scientific basis for further study of the process of CH₄ emission from permanently flooded paddy fields throughout a year and to explore effective mitigation options for CH₄ emission in more detail.