Continuously improving freshwater aquaculture efficiency will promote the sustainable development of freshwater aquaculture, which is crucial to ensure aquatic food supply. In particular, measuring the total factor productivity (TFP) of freshwater aquaculture to find ways to improve its efficiency is of great significance to sustainable development of freshwater aquaculture industry. Therefore, based on directional distance function, this paper constructs a meta-frontier Malmquist index (MMI) model by considering the regional heterogeneity to evaluate the TFP of freshwater aquaculture of China from 2004 to 2019. The results show that (1) from the perspective of time, TFP fluctuated significantly from 2004 to 2012, while after 2013, TFP remained around 1 with small fluctuation. In other words, freshwater aquaculture in China began to maintain a relatively negative state of development. (2) From a regional point of view, this study found that freshwater aquaculture TFP of inland region is better than the TFP of coastal region. (3) From the decomposition index, the variation of freshwater aquaculture TFP was driven by the combined effect of technology change (TC) and technical efficiency change (EC). In addition, the decomposition index efficiency shows that the technical efficiency decreases and the management efficiency changes little. (4) The gap of freshwater aquaculture technology in coastal areas is very small, and close to the optimal technical level. While in inland region, on the contrary, there is more room for improvement. According to the above empirical results, this paper finally gives some policy suggestions to improve the TFP to ensure the sustainable development of freshwater aquaculture.