The sustainability of rice-cropping systems hinges on balancing resources, output, and environmental impacts. China is revitalizing the ancient ratoon rice (RR) system for input savings and environmental benefits. Prior research has explored the RR system’s performance using various individual indicators, but few studies have focused on its overall balance of these factors. Environmental efficiency (EE) analysis addresses this gap. Using field survey data from Hunan Province in China and the slacks-based data envelopment analysis method, we quantified the EE of the RR, double-season rice (DR), and single-season rice (SR) systems. Key findings include: (1) the RR system outperforms in carbon emissions and non-point source pollution; (2) the RR system’s EE is 0.67, significantly higher than the DR (0.58) and SR (0.57) systems, indicating superior performance; and (3) despite its relatively high EE, the RR system can still improve, mainly due to input redundancy and production value shortfall. These findings provide strategies for optimizing RR systems to enhance agricultural sustainability.