Decoupling carbon emissions from economic growth is the key for the sustainable development of developing countries. Based on the panel data of marine aquaculture in China from 2010 to 2019, this paper employs the Tapio decoupling index model to analyze the decoupling characteristics of net carbon emissions and the economic growth of marine aquaculture. The logarithmic average weight decomposition method (LMDI model) and Tapio decoupling effort index model are also introduced to explore the contribution of various areas, provinces, and factors to the decoupling of net carbon emissions and the economic growth of marine aquaculture. Empirical results show that: (1) Net carbon emissions have a decoupling trend from the economic growth of marine aquaculture, but there is a large regional difference. (2) Regarding the degree of decoupling efforts, it is much stronger in the eastern and southern ocean economic zones than that in the northern ocean economic zone. (3) In terms of the decoupling contributions of various factors, carbon emission intensity > aquaculture scale > aquaculture efficiency > aquaculture structure, but there is heterogeneity among the different regions. Among the reasons for the inter-regional differences, carbon emission intensity > aquaculture scale > aquaculture structure > aquaculture efficiency. A further redundancy efficiency analysis explains the source of the differences. On this basis, strategies are proposed to improve the efficiency of marine aquaculture, including the construction of a modern three-dimensional aquaculture system, the improvement of the market-oriented mechanism, and the establishment of a modern marine aquaculture economic system.