Permanently flooded rice fields, widely distributed in south and south-west China, emit more CH4 than those drained in the winter crop season. For understanding CH4 emissions from permanently flooded rice fields and developing mitigation options, CH4 emission was measured year-round for 6 years from 1995 to 2000, in a permanently flooded rice field in Chongqing, China, where two cultivations with four treatments were prepared as follows: plain-cultivation, summer rice crop and winter fallow with floodwater layer annually (convention, Ch-FF), and winter upland crop under drained conditions (Ch-Wheat); ridge-cultivation without tillage, summer rice and winter fallow with floodwater layer annually (Ch-FFR), and winter upland crop under drained conditions (Ch-RW), respectively. On a 6-year average, compared to the treatments with floodwater in the winter crop season, the CH4 flux during rice-growing period from the treatments draining floodwater and planting winter crop was reduced by 42% in plain-cultivation and by 13% in ridge-cultivation (P < 0.05), respectively. The reduction of annual CH4 emission reached 68 and 48%, respectively. Compared to plain-cultivation (Ch-FF), ridge-cultivation (Ch-FFR) reduced annual CH4 emission by 33%, and which was mainly occurred in the winter crop season. These results indicate that draining floodwater layer for winter upland crop growth was not only able to prevent CH4 emission from permanently flooded paddy soils directly in the winter crop season, but also to reduce CH4 emission substantially during the following rice-growing period. As an alternative to the completely drainage of floodwater layer in the winter crop season, ridge-cultivation could also significantly mitigate CH4 emissions from permanently flooded rice fields.