With the rapid development of economy and society and the continuous progress of science and technology, the public demand for marine products and services is increasing, and the marine economic and social benefits are rising. It is very important to improve the management level of marine economy. The purpose of this study is to analyze the comprehensive management and coordination mechanism of China’s marine economy. This study selects Lianyungang City as the research object and takes the marine economic data from 2010 to 2019 as the research data. This study establishes three evaluation index systems of marine economic development. Then, according to the influence of the marine industry development, social development, population, marine resources and environment, regional scientific and technological innovation ability, government comprehensive management, and other factors on the regional marine economic management, this paper puts forward a set of marine economy comprehensive coordination management system and method and evaluates the current situation of marine economic development in Lianyungang City. The results show that, in the 10 years from 2010 to 2019, the comprehensive management evaluation value of China’s marine economy has increased from 0.20 to 0.33, with an average annual increase of 6.57 percentage points. The system level has been upgraded from the initial “poor” to “average,” achieving rapid growth. It is concluded that the index system evaluation of this study well reflects the change of the management level of China’s marine economy and has a promoting effect on the development of China’s marine economy, making contributions to China’s economic management.