Livestock manure heaps and wetland rice fields are major sources of CH4 emissions. A field experiment with an associated composting study were undertaken to investigate CH4 emissions during manure composting and subsequent land application on paddy. Over a 24-day period in the composting experiment, CH4 emissions from stored manure was 17 times higher than that from composting manure, indicating that composting as an aerobic process was effective in mitigating CH4 emissions compared with manure storage, which is normally under an anaerobic environment. Stored and composted manures were subsequently applied as organic fertilizers in the field experiment. Compared with the non-fertilized control treatment, stored and composted manures increased grain yields by 30% and 21%, respectively. During the full rice-growing season, the cumulative CH4 emission was 15.8 g CH4/m2 with the application of composted manure, only one-third of that from stored manure. CH4 emission per unit of grain yield was significantly decreased by composted manure, with a reduction of 56% from the control and 73% from stored manure. The results indicate that composted livestock manure in rice cultivation is a triple-win option through sustaining rice yield, mitigating CH4 emissions and re-utilizing livestock waste.