The effect of biochar application on the net ecosystem carbon budget (NECB) and the mechanism controlling methane (CH4) emission in paddy soils under vegetable–rice rotations are poorly understood. A 2-year field experiment was conducted with three treatments: control (no fertilizer or biochar application), chemical fertilizer (BC0) and biochar plus chemical fertilizer application (BC1) to analyze greenhouse gas (GHG) fluxes, soil organic carbon (SOC) content, as well as the abundance and community structure of methanogens and methanotrophs in a vegetable–rice rotation. Biochar addition (BC1) did not affect the yield, or the emission of total CH4 or nitrous oxide (N2O) but significantly increased carbon dioxide (CO2) emission as compared to BC0 in the vegetable season. Rice yield in BC1 was 14.1 % higher than in the control but was lower than in BC0 because of lower available nutrients in BC1 than in BC0. During the rice season, cumulative CH4 emission under BC1 was increased by 2.65 times as compared with BC0 (P < 0.01), in association with an increase in methanogenic and decrease in methanotrophic gene abundances. The cumulative CO2 emission was not different between BC0 and BC1 while cumulative and yield-scaled N2O emissions were significantly higher in BC1 than in BC0 in the rice season. However, BC1 increased SOC and NECB, but decreased the ratio of carbon (C) emission to C sequestration, net global warming potential (NGWP) and greenhouse gas emission intensity (NGHGI) as compared to the BC0 and control treatments (P < 0.01). The increase in GHG emissions in the biochar-amended soil was compensated by the increase in soil C storage and C uptake by rice, based on NGWP and NGHGI. The increase in NECB and SOC in the BC1 treatment indicates the benefit of biochar in restoring SOC during the rice season. This study provides insights into the effects of biochar addition on changes in bacterial abundance and community structure which increased CH4 emission in the rice season of a vegetable–paddy rotation.