To solve the problems of poor integration of business systems, opaque assembly process, and untimely exceptions handling, an aircraft assembly line digital twin system for layered and transparent supervisory control is proposed. After the requirements analysis, a four-tier architecture is proposed, namely physical layer, twin data layer, twin model layer and application layer. And three core functional modules are designed and implemented, including twin database construction for multi-dimensional data integration, final assembly lines digital twin modeling for transparency and visualization, integrated hierarchical supervisory control for on-site exception handling. The practical application shows that proposed system meets the requirements of multi-level, multi-dimensional, multi-role distribution remote supervisory control and comprehensive analysis, and effectively improves the digital and transparent level of aircraft final assembly.