Water transfer megaprojects (WTMPs) adapt arid regions to climate-driven water scarcity by diverting freshwater, potentially enhancing carbon sequestration through aquatic ecosystems restoration. However, their potential to mitigate climate change has not yet been explored. Here we propose a WTMP-based climate mitigation framework that integrates the long-lived mega water infrastructures with food, water, and energy sectors. The applications of our framework to China's South-to-North Water Transfer Project (SNWTP) demonstrate that WTMPs can help mitigate climate change through enhancing food security and promoting energy transition. Our framework highlights three key findings: (1) the median annual net primary production (NPP) sum of irrigated crops across the pan-North China Plain increased by 4.39 % between 2015 and 2021 (84.79 million tons) relative to 2007-2014 (81.22 million tons); (2) the enhancement of crop NPP boosts the production of crop residue-based biochars (approximately 75 million tons annually) that can avoid similar to 187 million tons of CO2 emissions annually after the SNWTP's operation; (3) SNWTP within a lifespan of at least 50 years can help promote the deployment of canal-based solar photovoltaic (PV) units with an installed capacity of approximately 80 GW, which could contribute to a 6.58 % increase for China's renewable energy and avoid 1495.23 million tons of CO2 emissions. Our research highlights the importance of exploring more untapped benefits of long-lived mega water infrastructures for climate mitigation when most of the existing low-carbon and negative emission technologies are still far from sufficiently deployed.