Virtual reality (VR) based on deepwater installation training provides new workers or inexperienced workers with rehearsing and training environment so that they can immerse themselves in this environment and improve their manipulative skills fast and efficiently. It can greatly cut down the training cost and decrease losses produced by mis-operations. In order to effectively achieve this training goal, it is crucial to express the response of multi-body system comprised of vessel, crane, cable and lifted equipment, truly and reliably. This paper proposes a mathematical model for the response analysis of multi-body system. The solution of the mathematical model for virtual simulation is also presented. The architecture of VR simulation system and the crane simulator are designed. A case study was performed to validate the feasibility of the proposed model. The results show the VR simulation training system has a high reality and response rate. This indicates the applicability of the proposed mathematical model and the VR system in deepwater installation simulation of subsea production facilities.