Implementation of the dual-fuel engine as ship main propulsion in Indonesia is low. There is a need for a study about the ship design process for dual fuel engine ship, especially for the engine room. Process and instrumentation diagram can’t give a whole picture of the real engine room, but three-dimensional can provide this. First, this study is to know about the process and instrumentation diagram on harbour tug diesel-LNG dual fuel engine 2 × 2500 HP. Second, this study is to know about the original, clustered, and reordered design structure matrix of all piping components. Third, this study is to know about three-dimensional design using modularization with rule-based algorithm. Components from the bilge & ballast system, oily water separator system, firefighting system, domestic supply and discharge system, marine diesel fuel oil system, LNG fuel oil system, lubricating oil system, cooling system, and compressed air system are inserted in original DSM. The rule-based algorithm is for clustering and reordering. At the end of the original, clustered, and reordered DSM there is a need for the objective function and sum value calculation. In this study, DSM modeler is used to do the clustering and reordering process included in one by clicked clustering algorithm feature. So, in this study is decided that reordering process is done manually using the workflow of the system to ensure that clustering algorithm feature can give clustered and reordered DSM, by compared the objective function and sum value from the original, clustered, and reordered DSM. The result of the objective function and sum value comparison always give less value than the original and clustered DSM. Clustered and reordered DSM had the same value. Sometimes the objective function and sum value of reordered DSM is greater than clustered DSM, which means there is human error when manually reordering the clustered DSM. Less value of the objective function and sum value DSM is used to create three-dimensional. Components that are included in one cluster need to be located nearly. Modularization with rule-based algorithm is applicable in three-dimensional design engine room layout.