Ratoon rice monoculture system (RR) is a labor-efficient and high-yielding cropping system in southern China. The rice–duck coculture system has been increasingly recognized as a mutually beneficial agricultural practice. However, the environmental impacts, economic performance, and sustainability of transitioning from a RR monoculture to a ratoon rice–duck system (RR-D) coculture remain unclear. A three-year (2022–2024) field experiment with three replications was therefore conducted in the Jianghan Plain, China (29°41′ N, 112°25′ E), to compare greenhouse gas (GHG) emissions, economic benefits, and emergy-based sustainability indicators between the RR and RR-D systems at a significant level of p < 0.05. The results showed that the RR-D significantly reduced CH₄ emissions by 25.7–39.5% but increased N₂O emissions by 18.7–122.2%. The average global warming potential (GWP) and GHG intensity decreased by 27.8% and 30.7%, respectively. Meanwhile, RR-D increased economic benefits by 131.0–167.1%, but lowered the unit emergy value per economic benefit (UEV_Benefits), renewable emergy ratio (%R), emergy yield ratio (EYR), and emergy sustainability index (ESI), and increased the environmental loading ratio (ELR). Overall, RR-D may improve economic returns and GHG mitigation, but its emergy-based sustainability requires optimization of feed, labor, and duck stocking density.