In this study, in order to investigate a modeling technique of the structure with bolted joints, four kinds of finite element model are introduced; a solid bolt model, a coupled bolt model, a spider bolt model, and no bolt model. All proposed models take account on prestrained effect and contact behavior of flanges to be joined. Among these models, a solid bolt model, which is modeled by using a 3-D solid element and a surface-to-surface contact element between the head/nut and the flange interfaces, has the best accurate responses compared with the experimental results. In addition, coupled bolt model, which couples the degree of freedom between the head/nut and the flange, shows the best effectiveness and usefulness in view of computational time and memory usage. Finally, the bolt model proposed here is adopted for structural analysis of a large diesel engine of a ship consisting of several parts which is connected by long stay bolts.