China's marine economy has entered the stage of high-quality development. Total factor productivity of the marine economy, as an important indicator reflecting the structural optimization, technological progress, and management innovation of marine development, is an important characterization of high-quality development level. The improvement of total factor productivity is not only driven by traditional factors such as capital and labor. Although the system theory and an overall perspective should be adopted to constantly explore and discover new drivers of marine economic growth, most of the existing studies are based on a single or a few limited driving factors. Most of them focus on traditional factors such as nature and material, and lack analysis of the common driving mechanism and effects of natural, intellectual, social, and institutional capitals on economic growth. Therefore, in order to explore the dynamic mechanism of total factor productivity of the marine economy, this study used a Translog-stochastic frontier analysis (SFA) model based on a transcendental logarithmic production function to measure the total factor productivity of the marine economy in coastal areas from 2000 to 2020, and identified the dynamic mechanism of development by constructing an evaluation indicator system including natural, intellectual, social, institutional, and external environment factors. The results showed that: 1) The average level of capital factor endowment increased steadily with a significant growth rate, and the accumulation rate of various types of capital generally presented a slow-fast-slow growing trend. The regional factor endowment of various types of capital was quite different. 2) The average total factor productivity of the marine economy was on the rise, which is at the medium level. The growth rate was slow, the regional difference was obvious, and growth showed certain path dependence. 3) The total factor productivity of the marine economy was mainly driven by natural capital in 2000-2012 and by intellectual capital in 2013-2020. The total factor productivity of the marine economy in the northern, central, and southern marine economic zones were mainly driven by natural capital from 2000 to 2012 and by natural, social, and institutional capital respectively from 2013 to 2020. The driving force of natural capital was decreasing, and the driving forces of intellectual, social, and institutional capitals were increasing. The research results can be used as a reference in formulating differentiated marine economic development policies.