The information model system is an important part of the research and application of BIM for port & waterway engineering. In order to solve the problems of model hierarchy disorder and difficult management in the application of BIM for port & waterway engineering throughout its life cycle，combining with the characteristics of the port & waterway engineering industry，this paper analyzes and studies the model system of port & waterway engineering BIM，puts forward the idea and specific method of building the model system for port & waterway engineering BIM in layers，and finally verifies the method of building the model system in layers based on the application of practical projects. The result shows that the hierarchical model system makes the hierarchical structure of the model clear and facilitates the standardized management and application of the information model.