A new technology may be biased towards saving energy, or reducing pollution emission or increasing economic output. It is necessary for the high-quality development of marine economy to promote environment-based technological progress. The purpose of this paper is to estimate the biased technological progress and its influencing factors of China’s marine economy from 2002 to 2016. We used a DEA-Malmquist model to measure the biased technological progress. Then we further analyzed influencing factors of biased technological progress. Our research found that the TFP of the marine economy was basically growing, and this growth was mainly due to a positive impact of technological progress. In general, the technological progress of marine economy is gradually biased towards energy conservation and emissions reduction. Furthermore, technological progress in the Yangtze River Delta are more conducive to energy conservation. The marine economic production in the Pan-Pearl River Delta is more inclined to promote production growth, while tit is most concerned about environmental protection in the Bohai Rim region. In addition, factors such as environmental regulation, economic level, FDI and industrial scale have different impacts on biased technological progress of marine economy. The results show that the directive regulations have a greater impact on the input-biased technological progress, while the incentive regulations have a greater impact on the output-biased technological progress. Therefore, this study has important guiding significance for energy conservation and emission reduction of marine economy in China. And the green development path of China’s marine economy can provide a reference for the development of European blue economy.