Against the backdrop of global warming and an increase in extreme weather events, the freshwater aquaculture industry, which is highly dependent on environmental conditions, faces severe challenges. As the world’s largest producer of freshwater aquaculture, the stability of China’s production is crucial for ensuring national food security and rural livelihoods. This study utilizes provincial panel data from China (2007–2023) and employs the HP filter separately for each province to construct a “climate-induced output” indicator. A panel data model is then established to examine the impact and transmission mechanisms of extreme climate risks on freshwater aquaculture output. The findings reveal the following: (1) Climate risks exert a significant negative impact on freshwater aquaculture production, with extreme low temperatures, droughts, and extreme rainfall having particularly pronounced effects. (2) Natural disasters play a partial mediating role between extreme climate and output, accounting for approximately 26.35% of the total effect. (3) From an overall perspective, both increased labor productivity and greater operational scale can significantly mitigate the negative impacts of climate risks. This study provides empirical evidence to inform policies on optimizing regional aquaculture layouts, enhancing climate resilience, and formulating adaptive strategies.