The rice–crab co-culture (RC) system is a multidimensional integrated farming model with significant potential for balancing ecological and economic benefits in paddy fields. However, improper nitrogen (N) fertilizer application exacerbates greenhouse gas (GHG) emissions, degrades water quality, and disrupts the balance of the RC ecosystem. Therefore, optimizing and improving N management strategies for the RC system is crucial to maximize its ecological and economic benefits. This study conducted a two-year field experiment to assess the impact of optimizing N application on the productivity, sustainability, and economic benefits in RC systems. Comparisons were made to compare rice and crab productions, GHG emissions, and net ecosystem economic benefit (NEEB) between the RC and rice monoculture (RM) systems under different N application rates (0, 150, 210, and 270 kg ha−1) with the aim of identifying the optimal N application rate for the RC system. The results showed that the N application rate of 210 kg ha−1 in the RC system improved the agronomic traits and N use efficiency, leading to a 0.4% increase in rice yield (7603.1 kg ha−1) compared to the maximum rice yield in the RM system at 270 kg ha−1. At this application rate, surface water quality was optimal for crabs, resulting in the highest crab yields (370.1 kg ha−1) and average weights (81.1 g). The lower N application reduced the greenhouse gas intensity (GHGI) of the RC system by 13.7% compared to the RM system. The NEEB at the optimal N application rate of 210 kg ha−1 in the RC system reached 8597.5 CNY ha−1, which was 1265.7% higher than that of the RM system at 270 kg ha−1. In summary, optimizing N application in the RC system conserves N fertilizer resources, increases rice and crab yields, and reduces GHG emissions, thereby synergistically enhancing both economic and ecological benefits. Optimizing the N application rate has greater potential in other innovative RC models, and the productivity, sustainability, and economic efficiency should be further investigated.
