The shipbuilding industry plays a pivotal role in national strategic security and economic development, and one critical challenge is the pipeline layout design problem. It predominantly relies on designers’ subjective experience, and it is marked by a lack of efficient knowledge sharing and the absence of smart pipe routing algorithms. This paper proposes an agile design system, which integrates ship pipeline design knowledge management, semi-automatic design that involves frequent interaction with human designers, and automatic rule checking. The framework is refined by digital twin concepts, facilitating close collaboration between physical and digital systems. The paradigm shift holds the potential to substantially enhance the efficiency of ship pipeline layout design, while concurrently reducing the reliance on manual labor.