In response to the complex integration of "three-in-one" systems in the production line of new energy vehicles, the long traditional physical debugging cycle, high cost, and low efficiency, a virtual debugging method for the production line of new energy vehicles based on digital twin is proposed. A three-layer integrated architecture of "physical entity-virtual twin-data interaction" is constructed to realize the digital mapping of the entire process of four major processes; an innovative multi-source data fusion engine is established to build a process optimization and error compensation model, and a three-level virtual debugging process of "pre-simulation-joint debugging-optimization" is formed. After verification on the production line of a leading automaker: the process optimization cycle is shortened from 3 to 6 weeks to 72 hours, the quality traceability time is compressed from 2 to 4 hours to 8 minutes, the accuracy of defect analysis reaches 92% to 95%, and the comprehensive energy efficiency and product qualification rate of the production line have been significantly improved. This method can provide a feasible and replicable technical path for the intelligent manufacturing of new energy vehicles.