To investigate the effects of water management on soil organic carbon (SOC) dynamics and carbon dioxide (CO₂) emissions in highaltitude paddy fields, this study established four water treatments in the Dali Erhai Basin: conventional flooding (W1), controlled irrigation (W2), controlled irrigation combined with 1/3H return flooding (W3), and controlled irrigation combined with 1/4H return flooding (W4), and systematically analyzed the changes in SOC content and CO₂ emission characteristics under different water management regimes. The results showed that different water management practices significantly affected SOC dynamics and CO₂ emission characteristics. The controlled irrigation combined with return flooding treatments maintained relatively high SOC content during the early and midtolate growth stages, especially in the 10-20 cm soil layer; SOC content decreased after drainage at the yellow ripening stage, but the W4 treatment showed the largest increase in deeplayer SOC at harvest (7.44% relative to pretransplant) and also had the highest average SOC content over the entire growth period. Although controlled irrigation (W2) favored shortterm accumulation of SOC in deeper layers, it was detrimental to the longterm stability of the surface carbon pool, and it resulted in the highest soil CO₂ emission flux due to frequent drying–rewetting cycles. The W3 and W4 treatments significantly reduced soil CO₂ emissions, with W4 having the lowest average soil CO₂ flux (80 mg·m⁻²·h⁻¹). Although the W3 treatment had the highest total CO₂ emissions due to vigorous plant growth, W4 achieved higher deeplayer carbon sequestration and lower soil CO₂ emissions while maintaining moderate total emissions (lower than W3). Based on comprehensive evaluation of SOC accumulation, profile distribution, and CO₂ emissions, W4 was identified as the water management regime with the best overall performance. This study provides a theoretical basis for optimizing water management strategies in highaltitude paddy fields and achieving synergistic effects between carbon sequestration and emission reduction.