Traditional agricultural systems are currently faced with the challenge of insufficient food production and reducing the negative effects of crop cultivation and population growth on the environment. One effective way to meet this challenge is the crop and animal co-culture in the paddy fields in South China. Rice-crayfish co-culture is the main component of such way, which has distinctive characteristics of deep waterlogging in off-rice season, total or partial direct straw return to fields, crayfish breeding in the whole year and strong crayfish burrowing, rapid planting area and high economic benefits. While the burrowing behavior of crayfish increases water-soil surface area, deep water management increases total dissolves oxygen and concurrently weakened methane transmission via bubbling. Although all the above measures theoretically reduce methane emission in paddy fields, the potential effect on global warming of rice-crayfish co-culture systems is not entirely clear. This study involved three treatments ― waterlogging in off-rice season (W), waterlogging in off-rice season with straw return (WS) and waterlogging in off-rice season with straw return and crayfish (WSC). The aim was to investigate the characteristics of methane (CH_4), nitrous oxide (N_2O) and carbon dioxide (CO_2) emissions under different treatments and to provide data support for accurate assessment of paddy greenhouse gas emission. The results showed that the cumulative CH_4 emissions were respectively (10.01.2) g*m~(-2), (9.22.8) g*m~(-2) and (12.71.2) g*m~(-2) under W, WSC and WS in 2015 and (28.55.2) g*m~(-2), (26.82.1) g*m~(-2) and (45.63.3) g*m~(-2) under W, WSC and WS in 2016. Compare with W, cumulative CH_4 emission under WS increased by 27.23% and 60.08% respectively in 2015 and 2016. Compared with WS, WSC decreased cumulative CH_4 emission respectively by 29.02% and 41.19% in 2015 and 2016. Cumulative CO_2 emission significantly increased under WS, compare with W in both years. There was only a slight effect on cumulative N_2O emission of WS and WSC compared with W. Rice yield was 8.81 t*hm~(-2) under WSC treatment and not different between W and WS treatments. Global warming potential (GWP) of WS significantly increased compare with W, and this increase was suppressed by WSC due to decreasing CH_4 emission. Then compared with WS, WSC treatment significantly decreased greenhouse gas intensity. There were no significant differences in soil dissolved organic carbon, acetic acid, NH_4~+-N and NO_3~--N contents among W, WS and WSC. Compare with W and WS, WSC considerably increased rice-crayfish co-culture benefits per unit area with less greenhouse gases emission.