As an important part of the world economy today, the marine economy is of great significance for promoting economic growth and sustainable development. To better promote the development of marine economy, the Augmented Dickey-Fuller (ADF) unit root test was first used to test the stationarity of marine economy related variables to ensure the reliability of the model. Then, the Vector Error Correction Model (VECM) is used to analyze the long-term stable relationship and short-term dynamic adjustment relationship between the marine industrial structure rationalization and the marine economic growth. These results reveal the mechanism of the influence of the rationalization of marine industrial structure on the growth of marine economy. It is found that among the eastern coastal provinces and cities, the rationalization level of marine industrial structure in Shanghai is up to 0.163 points, which is higher than other cities. The main reasons are the low specialization index of marine labor force, the comprehensive utilization amount of industrial waste in 10,000 yuan of gross marine product, the low environmental protection index, and the large gap between the benefits of each index. In addition, the study also found that the Granger causality test values of the delayed combination of variables Gross Ocean Product (GOP), ts, GOP, and ts were 5.531, 14.672, and 15.069, respectively. Finally, it is found that the upgrading of marine industrial structure and the output of marine economy will correct the deviation of industry rationalization below the equilibrium value in the short term at a rate of 0.1675. According to the above results, the study puts forward the following suggestions. First, it needs to strengthen the planning and layout of the marine industry, rationally guide the allocation of resources and industrial development. Second, it needs to increase support for scientific and technological innovation, and promote technological progress and industrial upgrading. The third is to strengthen the government's policy support and supervision to provide a stable policy environment and market environment for industrial development. The innovation lies in the systematic study of the relationship between the rationalization of marine industrial structure and the growth of marine economy.