Prefabricated building projects represent industrialized and intelligent construction through factory production, standardized design, and mechanized assembly. This study presents a multi-agent simulation approach to model the prefabricated construction process, allowing for the concurrent optimization of the prefabricated component (PC) splitting design and the construction organization plan through iterative simulation. (1) Employing a questionnaire survey, it identifies critical factors affecting schedule and cost from a design–construction coordination perspective. (2) Based on these findings, an agent-based model was developed incorporating PC installation, crane operations, and storage yard spatial constraints, along with interaction rules governing these agents. (3) Data interoperability was achieved among Revit, NetLogo3D and Navisworks. This integrated environment offers project managers digital management of design and construction plans, simulation support, and visualization tools. Simulation results confirm that a hybrid resource allocation strategy utilizing both tower cranes and mobile cranes enhances resource leveling, accelerates schedule performance, and improves cost efficiency.