Objective The objective was to obtain water and nitrogen management mode for methane (CH₄) emission reduction, and reveal the effects of soil organic carbon fraction and methane oxidizing bacteria on CH₄ emission flux from rice fields treated by different irrigation methods and nitrogen application.Method Through field experiment, CH₄ emission fluxes, soil organic carbon fraction contents and methane oxidizing bacteria numbers at different growth stages of double-cropping rice were determined under three irrigation methods (conventional irrigation, “thin-shallow-wet-dry” irrigation and alternate drying and wetting irrigation) and three nitrogen application methods (N1: 120 kg·hm^-2 nitrogen, 20% basal fertilizer and 80% topdressing; N2: 120 kg·hm^-2 nitrogen, 50% basal fertilizer and 50% topdressing; N3: 90 kg·hm^-2 nitrogen, 50% basal fertilizer and 50% topdressing). The correlation relationships of CH₄ emission fluxes with soil organic carbon fractions and methane oxidizing bacteria were analyzed.Result The treatment of alternate drying and wetting irrigation combining with N3 had the lowest CH₄ emission flux from rice fields, and CH₄ emission flux at the tillering stage of late rice decreased by 70.5% compared with the treatment of conventional irrigation combining with N1. Under the alternate drying and wetting irrigation, the soil microbial biomass carbon content at the booting stage of early rice in N2 treatment increased by 23.5% compared with both N1 and N3 treatments, and the soil soluble organic carbon content at the tillering stage of late rice in N3 treatment increased by 12.0% and 12.9% compared with N1 and N2 treatments, respectively. Under the N3 treatment, conventional irrigation increased the soil readily oxidizable organic carbon content by 38.8% and 40.9% compared to “thin-shallow-wet-dry” irrigation and alternate drying and wetting irrigation at the booting stage of early rice, respectively. CH₄ emission flux from double-cropping rice fields was significantly positively correlated only with soil soluble organic carbon content (r=0.55, P<0.01).Conclusion Soil soluble organic carbon content significantly affects CH₄ emission fluxes from double-cropping rice fields, and alternate drying and wetting irrigation combining with N3 treatment had lower CH₄ emission flux from rice fields.