The supply chain in the construction industry faces numerous risks during the holistic construction process due to complex materials management and intricate relationships among stakeholders. Risk management is essential for stakeholders to effectively operate supply chains and avoid unpunctual deliveries. This paper presents a supply chain risk management strategy that uses a digital-twin enabled construction system with Kanban. With the advent of Industry 4.0, technologies such as the Internet of Things (IoT), big data, and artificial intelligence have emerged in supply chain management. These technologies are applied in Digital twin to precisely connect the physical and virtual worlds and achieve deep synchronization. It monitors the supply chain networks and ensures the visibility of risks. Kanban is a lean approach that intuitively displays the operational parameters and decision-making support. The warning mechanism on Kanban utilizes Gaussian Mixture Model (GMM) with probabilistic density fitting (PDF) of historical data to predict delays. The results show that the possibility of false positives is less than 15% before five days of arrival. As the forecast days get shorter, the accuracy rate will increase. The reflection of the Digital twin enabled construction system contributes to the research and practical supply chain risk management.