Recently, world leading companies on manufacturing field are trying to adopt a PLM methodology, which is a new production paradigm, for a survival and strengthening the competitiveness. Some projects for a digital shipyard including a methodology of a digital simulation framework are going on by Seoul national university and Samsung heavy industry. A Database methodology for a scheduling data, an interfacing methodology for a simulation input and output, and a synchronized simulation related methodology are required for enhancing the value of the digital simulation for shipbuilding. In this paper, such a methodologies and a related case study for a fabrication factory and an assembly factory are presented.