Rice–crayfish farming systems (RCs), a novel rice cropping system, have gained rapid popularity in many countries due to their economic advantages. Fertilizers tend to be applied in large quantities for higher profits, but has high burden on resources and environment, especially in terms of the carbon emissions. It is crucial to explore an optimal fertilization strategy with high productivity and low carbon emissions for the sustainable development of RCs. However, information about C emissions is incomplete, regarding the indirect C emissions during the rice growing season as well as C emissions during the crayfish culture period. We conducted field experiments to investigate the effects of five fertilization strategies including no fertilization (CK), farmer’s practices (FP), optimized fertilization (OPT), organic fertilization only (OF), and organic fertilizer substitution (OPTOF) on the productivity, economic benefits, greenhouse gas (GHG) emissions, carbon footprint, and sustainability index of RCs. Results showed that OPT reduced direct (by 6.7%) and indirect (by 37.0%) GHG emissions during the rice growing season while maintaining rice (95%) and crayfish (104%) yields compared with that of FP. Additionally, the soil organic carbon storage and annual economic benefit of the OPT increased by 20.1% and 4.7%, respectively, whereas the carbon footprints of unit area, unit grain yield, unit energy yield, and unit of economic output decreased by 29.5%, 27.2%, 24.5%, and 32.7%, compared to the FP, respectively. The sustainability index (0.78) of the OPT treatment was significantly higher than that of other treatments due to its higher productivity and lower the carbon footprint. In conclusion, optimal fertilization strategy in RCs could achieve to increase productivity while reducing carbon footprint. This is conducive to the sustainability of RCs. Future attention in RCs should be focused on the development and promotion of such strategies.

水稻-小龙虾养殖系统（RCs）是一种新型的水稻种植系统，由于其经济优势在许多国家迅速普及。化肥往往为了获得更高的利润而大量施用，但对资源和环境的负担很大，特别是碳排放。探索高产、低碳排放的最优施肥策略对于RCs的可持续发展至关重要。然而，关于碳排放的信息并不完整，包括水稻生长季节的间接碳排放以及小龙虾养殖期间的碳排放。通过田间试验，研究了不施肥（CK）、农民实践（FP）、优化施肥（OPT）、仅施有机肥（OF）和有机肥替代（OPTOF）5种施肥策略对生产力、经济效益的影响。 RC 的效益、温室气体 (GHG) 排放、碳足迹和可持续性指数。结果表明，与FP相比，OPT减少了水稻生长季节直接（减少6.7％）和间接（减少37.0％）温室气体排放，同时保持了水稻（95％）和小龙虾（104％）的产量。此外，OPT土壤有机碳储量和年经济效益分别增长20.1%和4.7%，单位面积、单位粮食产量、单位能源产量、单位经济产出碳足迹下降29.5%，与 FP 相比分别为 27.2%、24.5% 和 32.7%。 OPT处理的可持续性指数（0.78）显着高于其他处理，因为它具有更高的生产力和更低的碳足迹。总之，RCs的最佳施肥策略可以实现提高生产力，同时减少碳足迹。这有利于RC的可持续性。区域委员会未来的注意力应集中在此类战略的制定和推广上。