In order to scientifically evaluate the level of economic development of ports in coastal cities, 20 coastal cities are selected, by constructing a comprehensive evaluation index system to do principal component analysis on port indicators, the calculated factor scores of ports in coastal cities are used as the original data, and the results obtained are classified by the method of cluster analysis, and the comprehensive port capacity of Shanghai, Shenzhen and Guangzhou are observed from the final analysis results are classified as the first category, among which Shanghai has the highest port transportation capacity, Guangzhou and Shenzhen are equal in terms of comprehensive port capacity, while the overall economic development of ports in coastal cities shows a large uneven phenomenon. Shanghai as the core of the Yangtze River Delta city cluster, Guangzhou and Shenzhen as the double core of the Pearl River Delta economic zone, the three cities and their ports are far ahead of other cities in the development of China's coastal cities, but some of the ports have not yet given full play to their own sea-side sea advantages, and the development potential needs to be further explored, for which corresponding countermeasures are proposed for the port development problems.