Including green manure into a rice-based double-cropping system has effects on both crop production and greenhouse gas (GHG) emissions. Yet, few studies have considered the trade-off between crop productivity, profitability, and carbon footprint (CF) in this cropping system of China. Thus, the impacts of different cropping regimes on crop productivity, economic benefits, carbon footprint, and net ecosystem economic budget (NEEB) were investigated. The treatments were rice–wheat (R–W), rice–rape (R–R), rice–hairy vetch (R–H), rice–barley (R–B), rice–faba bean (R–F), and rice–fallow (R). Compared to R–W treatment, planting rape (R–R), green manure (R–F, R–H), or fallow (R) in winter season tended to improve rice yield, but they were not conducive to yield stability. Treatments of R–H, R–F, and R reduced both direct and indirect GHG emission, and thus mitigated the area-scaled carbon footprint by 34.4%, 44.2%, and 49.7%, respectively, compared to R–W treatment. The economic benefits under R–R, R–B, or R system were not different from those of R–W treatment, while R–H reduced the economic benefit by 70.1%. In comparison with R–W treatment, R–H treatment reduced the NEEB, while R–F significantly increased the NEEB by USD 4065 ha−1. The present results indicate that as a measure to realize the combination of food security and environmental cost reduction, substituting leguminous crops with wheat can mitigate carbon emissions while ensuring profitability, on the premise of yield stability.