In order to reduce the coupling degree of the MDO (Multidisciplinary Design Optimization) model of ships，and thus to indirectly improve the optimization efficiency，a remodeling method for modeling is proposed based on a relation information flow-based clustering algorithm． In this algorithm，an exponential function is used as the substitution of the linear function to improve the theoretical hypothesis and the calculation method，and the co-ding of the algorithm is also modified． Moreover，two assessment indexes，namely the proportion of relation weight in the interior of the clustering and the BUS clustering scale，are proposed for comparison． Finally，a conceptual model of a 5400TEU container ship in the early conceptual design is used to illustrate the proposed modeling method．The results verify the feasibility of the method in ship modeling．