Recently, physics-based simulation plays an important role to check the risks induced by dynamic effects in advance. However, the existing programs had some limits to simulate design, production, and installation of ships and offshore structures. This study proposed physics-based simulation framework to integrate several physical theories efficiently. Based on the proposed framework, this study developed SyMAP (SyDLabs Multibody Analysis Program), which is a dedicated and differentiated program for ships and offshore structures. SyMAP can solve the equations of motion of rigid and flexible bodies. Furthermore, it has the scenario manager and user-friendly GUI. To verify the efficiency and applicability of the developed program, we present several applications such as topside module erection, thin plate block lifting by the floating crane, transportation of the mega block using modular transporters, etc.