In order to solve the problem of collecting necessary data affecting fuel consumption and building an intelligent energy efficiency system, this paper makes an in-depth study on the management of cross ship energy efficiency on the basis of program configuration generation. Firstly, this paper studies three methods: technology-driven analysis, support vector machine method, and energy efficiency evaluation method. In order to improve the functions of energy management, energy efficiency analysis, and auxiliary decision-making, this paper constructs a comprehensive intelligent scheme for the best ship navigation energy efficiency from the aspects of ship operation guidance, navigation performance evaluation suggestions, and shipping management decision-making, so as to meet the higher-level management needs of interested parties for ship energy efficiency. Among them, energy efficiency online monitoring can collect energy efficiency data and serve the other three functions, mainly monitoring ship energy consumption, environment, navigation, and other parameters. Energy efficiency evaluation is based on the data collected by online monitoring, and the results of ship energy consumption are obtained by using data mining technology. Through experiments and research, under the background of green, efficient, and intelligent ships, ship shore collaboration is an effective way to improve the ship’s energy efficiency management ability. Intelligent ships provide a new development path for strengthening the application service of ship energy efficiency management system.