The hierarchical structure of the computerized model of a ship blocks has an important role in understanding the internal structure of the block and determining the connection relationship between structural members inside the block. A model with only geometric information in the initial design stage evolves into a complex hierarchical structure containing a large amount of production information as the design stage progresses. Since the hierarchical structure is created manually through the empirical method of experts, it is difficult to define a consistent standardization method because each expert can express a different hierarchical structure. In addition, when a block model in a CAD system is converted into another CAD platform, serious problems are found in that production information is frequently lost and the hierarchical structure changes after conversion. To solve such a problem, it is urgent to easily create a hierarchical structure of a model by maximally utilizing geometric information existing in a CAD file. In this paper, we introduce an algorithm that automatically creates a hierarchical structure of blocks based on the shipyard assembly process using geometric information extracted from a neutral CAD format. The cost is calculated according to the connection relationship between the structural members, and then the complete adjacency graph is generated by applying the assembly priority function. After generating a minimum spanning tree (MST) for each set, a final hierarchical structure is created through clustering between adjacent nodes with similar costs. It was made possible to create a customized hierarchical structure in a form suitable for the work environment of the shipyard or the designer’s intention. The accuracy of the generated block hierarchy is verified through consultation with block division experts in shipyards. By applying the proposed algorithm, the block hierarchy generation, which was previously done manually, is performed in real-time. Also, the hierarchical structure of blocks lost in the CAD format conversion process can be restored only with geometric information. The proposed algorithm increases the efficiency of the subsequent designs by providing a right tool for verifying the consistency of the block model.