Achieving the targets of “carbon peak” and “carbon neutrality” has become a critical global mission, particularly for China, considering its abundant potential in hydropower resources. This research examines the practicality of integrated water-carbon optimization for cascade reservoirs in flood seasons, to facilitate green transformation and long-term sustainable development. A coordinated reservoir optimization methodology was proposed to enhance the synergy between hydropower generation and greenhouse gas emission reduction, while also guaranteeing flood control safety. The NSGA-II algorithm was applied to formulate multi-objective optimization scheduling schemes, complemented by a novel VIKOR-based multi-criteria assessment framework. The research specifically addressed cascade reservoirs situated in the lower Jinsha River basin, namely Wudongde, Baihetan, Xiluodu, and Xiangjiaba, analyzing representative flood events including those with multiple peaks (1966), early peaks (1974), and late peaks (1993), to evaluate hydropower generation and carbon emissions under various operational scenarios. Findings demonstrate that the NSGA-II-based optimal solution enhances hydropower production benefits while concurrently reducing greenhouse gas emissions. Compared with conventional operational strategies, the proposed method increased electricity generation by 6.178% and decreased greenhouse gas emissions by 20.312%, without compromising flood safety. Additionally, multi-criteria decision-making analysis using the VIKOR method suggests that decision-makers can select optimized scheduling schemes tailored to specific flood characteristics to enhance comprehensive performance. The proposed approach provides a flexible and sustainable management strategy for large-scale cascade reservoir operations.