Paying attention to the mechanisms of the GTFP of the marine economy and designing a scientific and reasonable optimization path are the keys to achieving a “win-win” balance between environmental protection and high-quality marine development. Therefore, this paper considers the rigid constraints of resources and negative environmental effects to construct a multi-factor evaluation model of the GTFP of the marine economy including capital, labor, and resources to expand the evaluation method system for the sustainable development of the marine economy. On this basis, this paper determines the influencing factors of the GTFP of China’s marine economy, qualitatively analyzes the mechanism of each influencing factor on the GTFP of the marine economy, uses multi-dimensional data of coastal areas, quantitatively analyzes the direct and indirect effects of the factors that influence the GTFP, and proposes practical optimization paths and safeguarding measures, which provide a decision-making reference for the implementation of China’s marine development strategy. The results showed that the GTFP of China’s marine economy was in a state of improvement and increased from 0.9878 in 2006 to 1.2789 in 2018. The direct effects of environmental regulations have a negative and significant impact on GTFP, whereas economic development, human capital, and technological innovations have a positive and significant impact on GTFP. In addition, environmental regulations have an “inclined N” double-threshold effect on GTFP. The impact of environmental regulations on the GTFP of the marine economy depends on the intensity of the environmental regulations, as different intensities of environmental regulations have different dominant levels of the “innovation compensation effect” and “offset effect” that affect the GTFP of the marine economy.