The 14th five-year plan emphasizes the importance of marine ecology and environmental protection, and the green concept is incorporated into the high-quality development system of the marine economy. This research used the data of 11 coastal provinces and cities in China from 2006 to 2016, based on the super-efficiency slack-based measure model and global Malmquist index model. The objective was to calculate the green total factor productivity (GTFP) of the marine economy, to study the impact of the evolution of the marine industrial structure on marine economic GTFP. The study found the following: (1) in general, the upgrade of marine industrial structure promoted the growth of marine economic GTFP and presented an inverted “U” trend of initially promoting and then suppressing. Spatially, only the advancement and rationalization of industrial structure in the Yellow and Bohai Sea regions inhibited the growth of marine economic GTFP. In terms of time, the advanced marine industrial structure promoted the growth of GTFP from 2006 to 2010, whereas that of industrial structure inhibited the growth of GTFP from 2011 to 2016. (2) The GTFP of the marine economy showed an increasing trend, but the conversion rate of production technology is low. Falling into the “efficiency trap” of highly advanced technology input and low-efficiency technology output should be avoided. (3) Affected by the mismatch of regional resources or industrial structure, government intervention showed an “opposite” mechanism in areas with different marine economic strengths. Government intervention in areas with higher marine economic strength was conducive to GTFP growth, whereas government intervention in areas with weaker marine economic strength would hinder GTFP growth.
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