Aiming at the deficiencies of the existing production management, debugging, production line flexible control and other aspects, this paper studies the virtual model construction, the synchronization behavior design, the interactive interface design, information analysis, production line flexible management and control around the processing of ship parts, using digital twin technology. The simulation evaluation, virtual debugging, synchronous operation analysis and flexible control of production line based on digital Twin are implemented. The research results have been popularized on trial in the shipyard, realizing automatic production and remote control of the ship's pipeline and production line, and reducing the number of shop staff by a large margin. The flexible control system can be used as a reference for other discrete manufacturing lines construction and the design of control system.