This paper conducts a simulation optimization study on the modular assembly process of large-scale special equipment for ships, which is difficult to achieve integrated transportation, installation, and rapid application due to its large size, weight, and complex structure. Firstly, the spatial interference, construction process, resource allocation, and time indicators involved in assembly operations were analyzed. Then, the 3D model and workflow model required for assembly operation simulation were constructed. Finally, Unity 3D and Plant-Simulation were applied for simulation development. The results indicate that the method of verifying the rationality of modular disassembly of equipment structure and the feasibility of construction process planning based on 3D model simulation is reasonable, and the method for optimizing operation time indicators based on random event process model simulation is feasible. The simulation results obtained in this article can provide data support for the construction decision-making of modular assembly of large-scale special equipment for ships, and the adopted technical route can provide methodological references for related engineering practice research.