How to realize the two-way development of marine ecological civilization and urbanization is an urgent problem in the construction and development of coastal cities. Therefore, this paper puts forward the method of coupling research on the two-way development of marine ecological civilization and urbanization in coastal cities. The method selects 20 evaluation indexes of marine ecological civilization construction from four aspects of marine resources endowment and marine system management, and 20 evaluation indexes of urban development from four aspects of population urbanization level and economic urbanization level, so as to jointly establish marine ecological civilization construction and cities in coastal cities. Based on entropy method to determine the weight of each index in the evaluation system, technique for order of preference by similarity to ideal solution method is used to improve the coupling coordination model to get the coupling coordination index, and uniform distribution function method is used to determine the coupling coordination level. In order to verify the performance of this method, the development level of marine ecological civilization and urbanization in 10 coastal cities was studied. The results show that from 2007 to 2016, the coupling coordination index of coastal cities has gradually increased from 0.5263 to 0.6406, which has obvious characteristics of regional agglomeration, showing a pattern of “East > South > North.” The difference between the coupling coordination index obtained by this method and the actual coupling coordination index is less than 0.0010. According to the research results, the paper puts forward suggestions to promote the economic development of coastal cities and the construction of marine ecological civilization and help realize the coordinated development of economic society and marine ecological environmental protection in coastal cities.