Rice and Azolla co-cultivation, an ancient rice cropping pattern in China, is a promising nature-based solution for reducing CH₄ emissions while maintaining high yields. However, the reduction potential and underlying mechanisms remain unclear when considering water management and N₂O emissions. This study investigated the comprehensive effects of rice and Azolla co-cultivation on both CH₄ and N₂O emissions through their influence on soil physicochemical properties, enzymes, and related functional genes, using a series of pot experiments with three irrigation regimes (AWD, 2 cm, and 5 cm flooding depth). Rice and Azolla co-cultivation reduced CH₄ emissions by 2.9 %-13.2 % across all irrigation regimes, with the most significant reductions observed at 2 cm and 5 cm flooding depths. Higher water depths were associated with higher CH₄ emissions. This reduction can be clearly attributed to the decrease in the abundance of mcrA, mcrA/pmoA, and β-1,4-glucanase, as well as the increase in the abundance of pmoA, Eh, and DO. Meanwhile, rice and Azolla co-cultivation had a reduction of N₂O emission by 1.7 %-8.6 %. Compared to AWD, 2 cm and 5 cm irrigation regimes greatly reduced N₂O emissions by 22.0 %-26.5 % and 35.2 %-39.7 %, respectively. It was observed that rice and Azolla co-cultivation decreased the abundance of AOA, AOB, nirS, protease, and nitrite reductase, while enhancing the abundance of nosZ and denitrification enzyme. Additionally, rice and Azolla co-cultivation enhanced the rice yield by 6.2 %-8.3 % under all irrigation regimes. Results confirmed rice and Azolla co-cultivation as a nature-based solution for low-carbon and high-yield rice planting, especially under 5 cm irrigation regime.