The development of the ports and cities in the Seto sea area has a great effect on the economic development of Japan. It is a typical case of harmonized development between the port and the city and is worthy of studying. To explore the relationship of port and the industry, cargo throughput and container throughput are used to represent the port development level. GDP and the number of employees are used to represent the industrial development level. Firstly, grey relational analysis method is used to calculate the correlation between ports and industries, and the grey correlations of each county are compared and the developing strategies of the Seto sea area are summarized. The results can bring an enlightenment to the development of the coastal economic zone of Liaoning province. Then, a comprehensive evaluation model is proposed, with both functionality and balance taken into account. So the main port indicator that has a great influence on the development of industries in the Seto sea area can be determined. It is cargo output. Lastly, results of the proposed model and the usually used models are compared. It shows that the model proposed is more realistic, and it can evaluate the relationship between ports and industries in the Seto sea area more accurately.