Integrated rice–aquatic animals culture systems (RACSs) are of interest in sustainability research because they have been found to host diverse species and there is potential for positive synergistic effects between the plant (rice) and aquatic animal culture. However, their effect on soil fertility, rice productivity, and greenhouse gas (GHG) emissions, as well as the associations among them, remain unclear. A meta-analysis was conducted to systematically evaluate the sustainability of RACSs from the perspective of “rice productivity–GHG emissions–soil fertility” and their associations and to clarify how environmental factors and fertilizer-management practices affect responses of rice yield and GHG emissions to RACSs. We conducted a meta-analysis of 1807 paired observations collected from 78 published papers covering four countries that compared soil fertility, rice yield, and GHG emissions in a conventional rice monoculture system (CRMS) and in a RACS. Overall, the RACSs improved soil structure (soil bulk density declined by 5.8 % and total and capillary porosity increased by 6.4 % and 5.7 %, respectively), increased soil organic carbon (C, 7.9 %) and nitrogen (N, 6.6 %) storage, and reduced CH4 (9.2 %) and N2O (4.5 %) emissions; rice yield were little higher (by 2.0 %) than that of the CRMS. However, the effects varied under different RACS modes, environmental factors, and fertilizer-management practices. For instance, compared to CRMS, yields were 4.1 % higher in the rice–duck mode, 3.9 % lower in the rice–crayfish mode, and the no significantly change in the rice–fish system. The effects on GHG emissions and soil fertility were more pronounced in the rice–duck and rice–crayfish modes than in the rice–fish mode. Furthermore, paddy soils with low fertility (lower soil organic C and N) and less nutrient (nitrogen and phosphorus) input provide a higher rice yield and lower GHG emissions under RACSs. Overall, the RACSs stabilized rice productivity and reduced GHG emissions by improving the soil structure and increasing soil C and N sequestration; however, the effects varied by different RACS modes, initial soil properties, fertilizer input rate, and climate conditions. As such, environmental factors and nutrient management should be considered when designing and deciding what type of RACSs to employ. Our results also highlight the great potential of RACSs in the development of sustainable agriculture practices in the context of climate change. Future research and applications should consider the response of RACSs to climate and environmental factors and fertilizer-management practices, to achieve greater production and environmental benefits.