Freshwater pond aquaculture is an important component of aquaculture system, and its input-output efficiency has always been a subject of concern. Based on the survey data of freshwater pond culture collected from 10 provinces, this paper analyzed the canonical correlation between input and output of freshwater pond aquaculture, coming to two main conclusions: (1) the correlation coefficient between output and input of freshwater ponds is 0.9613; (2) the efficiency is quite different among these 10 provinces, and the output-input ratio ranged from 0.76 to 1.65, with Zhejiang Province being the highest and Liaoning Province the lowest. Finally, some countermeasures have been proposed to promote sustainable development of freshwater pond aquaculture, including putting more efforts to the transformation and standardization of low-yielding ponds, constructing ecological farming model, enhancing the organization level of freshwater pond cooperatives, etc...