Agricultural fields, including rice (Oryza sativa L.) paddy fields, constitute one of the major sources of atmospheric methane (CH4) and nitrous oxide (N2O). Organic matter application, such as straw and organic fertilizer, enhances CH4 emission from paddy fields. In addition, rice straw management after harvest regulates CH4 emissions in the growing season. The interaction of tillage times and organic fertilizer application on CH4 and N2O emissions is largely unknown. Therefore, we studied the effects of fallow-season tillage times and fertilizer types on CH4 and N2O emissions in paddy fields in Ehime, southwestern Japan. From November 2011 to October 2013, four treatments, two (autumn and spring) or one (spring) in the first year, or two (autumn and spring) or three (autumn, winter, and spring) in the second year times of tillage with chemical or organic fertilizer application, were established. Gas fluxes were measured by the closed-chamber method. Increasing the number of tillage times from one to two decreased succeeding CH4 emission and the emission factor for CH4 (EFCH4) in the rice-growing season, suggesting that the substrate for CH4 production was reduced by autumn and spring tillage in the fallow season. Higher EFCH4 [1.8-2.0kgcarbon (C)ha(-1) d(-1)] was observed when more straw was applied (6.9-7.2Mgha(-1)) in the second year. Organic fertilizer application induced higher CH4 emission just after the application as basal and supplemental fertilizers, especially at a lower straw application rate. This indicated that EFCH4 in the organically managed fields should be determined individually. Organic fertilizer application with two tillage times induced N2O efflux during the rice-growing season in the second year, but N2O emissions were not affected by winter tillage. Although paddy fields can act as an N2O sink because of reduced soil conditions when straw application was high, application of organic C and nitrogen as fertilizer can enhance N2O production by the denitrification process during the growing season, especially in the ripening stage when soil anaerobic conditions became moderate. These results suggest that negative emission factors for N2O (EFN2O) can be applied, and EFN2O of organic fertilizer should be considered during the estimation of N2O emission in the paddy field.