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Agricultural intensification has greatly increased yields but has also negatively affected the environment. The coupling of two agricultural systems (i.e., integrated agriculture-aquaculture or integrated crop-livestock) has been proposed as one of the important ways that reduce the negative effects of agriculture on the environment, but large-scale experimental data are lacking. In this study, we examined the coupled rice-crab system, which is a rapidly developing rice-fish system in China. We conducted a field survey across several rice-planting areas and field and mesocosm experiments to determine whether the rice-crab system achieves high yields of both rice and crab without damaging the environment. Our field survey showed that rice yield was not reduced in the rice-crab system across four rice-growing areas although total fertilizer N was reduced compared to rice monoculture. Our field experiment also showed that the rice-crab treatment produced higher rice yield than rice monoculture treatment with the same fertilizer N application, and that the coupled rice-crab treatment had higher crab yield with less crab numbers of precocious maturation than the crab monoculture treatment with the same amount of feed. Both field and mesocosm experiments showed that the rice-crab system did not cause serious feed-N accumulation in the field. Isotope 15N labeling indicated that rice plants used 7.6% of the feed-N. Dual isotope 13C/15N analysis showed that 59.1% of the food consumed by crabs consisted of organisms that thrived by directly using nutrients in the field. This recycling of N within the field explains the low fertilizer-N input and low effluent-N in the coupled rice-crab system. Our results suggest that the coupling of rice with fish production can achieve synergies between food production systems to reduce environmental impacts per unit of production.