Digital Twin (DT) is considered to be the general purpose technology of the 4th industrial revolution, and realizing its engineering application universality is the common endeavor objective of both universities and companies. Based on the theoretical framework and technical route of DT, this paper focuses on its application exploration for new energy ships. Via blending technologies of cloud computing, open source software, the marine control system and characteristics of new energy, authors carry out a feasibility analysis from the shipboard and cloud architecture and implementation plan respectively. A DT of propulsion system is developed, deployed and operated online on a new energy ship (NES). Meanwhile, the DT data is used to correct the calculation deviation of the battery State of Charge (SOC) by the ship’s physical system. The research in this paper will provide a decision-making platform for situations such as safe operation, fault diagnosis, and condition-based maintenance, and also provide an effective solution for future DT system design of new energy ships.