Abstract: Paddy fields are one of the major sources of greenhouse gases emissions. Rice-animal co-culture systems play an important role in increasing rice yield and reducing greenhouse gases emissions, with their effectiveness being influenced by factors such as different rice cropping patterns, aquatic animal species, stocking densities, and nitrogen application rates. Based on 248 sets of field experiment data from 76 articles published between 2000 and 2025, a Meta analysis was conducted to evaluate the effects of rice-animal co-culture systems on rice yield and greenhouse gases emissions in China, and a random forest model was used to quantify the relative importance of different influencing factors. Based the data from different rice-animal co-culture sytems, compared with rice monoculture, rice-animal co-culture systems were found to significantly increase rice yield by 8.16% and reduce CH₄ emissions by 16.46% (P<0.05), while the reduction in N₂O emissions was not significant. Among these systems, the rice-duck co-culture system demonstrated superior effects on rice yield increase and CH₄ emission reduction compared to the rice-shrimp and rice-fish co-culture systems. The effects of co-culture systems on rice yield increase and emission reduction varied under different stocking densities, nitrogen application rates, soil properties, and climatic conditions. A greater rice yield increase (13.02%) was observed in co-culture systems with a nitrogen application rate of 0−120 kg/hm² compared to that (11.78%) with 120−240 kg/hm², while the latter showed a greater advantage in CH₄ emission reduction. Increasing duck stocking density was found to reduce the yield-increasing effect of co-culture systems, whereas increasing shrimp or fish stocking density was found to enhance or promote this effect. An initial soil organic carbon content of 0−20 g/kg was found to be conducive to a greater yield-increasing effect of co-culture system but was unfavorable for CH₄ emission reduction. Annual average precipitation of 1000−2000 mm was found to favor both the yield-increasing effect and CH₄ emission reduction in co-culture systems, whereas higher temperatures (annual average temperature≥20 °C) showed the opposite effect. The results of the random forest model indicated that the yield-increasing effect of co-culture systems was significantly influenced by nitrogen application rate, initial soil organic carbon content, stocking density, and annual average temperature (P<0.05 or P<0.01), while CH₄ emissions from paddy soils were significantly influenced only by annual average temperature. In conclusion, rice-animal co-culture systems in China were influenced by multiple factors, including annual average temperature, annual average precipitation, nitrogen application rate, initial soil organic carbon content, and stocking density. Under suitable climatic and soil conditions, optimizing rice cropping patterns, stocking densities, and nitrogen application rates can help achieve the dual goals of increasing yield and reducing emissions in paddy fields.