Digital twin (DT) has been around for many years, but there is no widely accepted standardized tool or method. In this study, system dynamics was proposed as a tool that can be integrated into multi-scale, multi-physics, and multi-disciplinary, which are continuously becoming issues in the DT field. Various heterogeneous data from multiple protocols or platforms could be integrated into one model. Through the five-step model building process, it was possible to integrate the theories and various models studied in the past. In this study, the operation and maintenance system of ROK Naval ships is implemented as a proposed method. Various physics, scales, and disciplines such as failures of ships, maintenance ability of repair shops and schedule pressure of mechanics were reflected. It was possible to observe non-intuitive correlations and potential problems caused by the latent effect of the high-fidelity DT model. The proposed method is also capable of updating through continuous data calibration or real-time interworking with external statistical analysis tools.