As off-shore prefabrication continues to gain momentum, supply chain management becomes increasingly complex for industrial modular construction projects and delays commonly occur to prefabricated modules. In order to make efficient utilization of limited module assembly resources (e.g., crews and bays) and reduce the waiting waste of materials on the module yard, a systematic optimization approach is desired to derive an optimal module assembly plan in coping with the dynamic supply chain and limited resource availability. By synthesizing information from the logistics management system, contract documents, and resources availability, a constraint programming based optimization algorithm is proposed. A case project abstracted from a real project is presented to demonstrate the feasibility and effectiveness of the proposed optimization approach. The information on module assembly start time, duration, and expected delivery time is generated to guide operations on the module yard. The minimum of total waiting time of materials on the module yard is derived for decision-making support. In conclusion, the proposed methodology seamlessly integrates principles of lean construction and constraints of resource scheduling into a constraint programming optimization formulation. This research potentially lends effective decision support to both crew work planning and materials logistical planning, ultimately leading to improvement on both construction productivity and logistical efficiency.