The subsea production control system, characterized by a complex and diverse structure and high cost, is one of the essential parts of a subsea production system. The rational layout of the subsea production control system is essential to reduce development costs and ensure safe production in offshore fields. Most previous studies on layout design in offshore fields have focused on the oil- and gas-gathering system. However, the layout of the subsea production control system has not thoroughly been researched to date and the seabed terrain and integral optimization have rarely been discussed. This paper focuses on the multi-layer star structure and multi-layer star-tree structure, two common layout structures of subsea production control systems, and establishes the corresponding model with obstacle and seabed terrain conditions. Obtaining the lowest possible total cost was the aim of the model. A hybrid algorithm combining the adaptive mutation particle swarm algorithm and the A-star algorithm was applied to integrally optimize the subsea distribution unit and umbilical touch down point positions, the pipe connection topology and pipe routes. The practicality of this approach is demonstrated by designing a layout with one FPSO and 22 subsea control modules. The results indicate that the multi-layer star-tree layout structure has a lower total cost compared to that of the multi-layer star layout structure. In addition, the results were compared with a case that ignores the seabed terrain, indicating differences in the total construction cost. This method provides engineers with quantitative references and reliable cost estimates to make decisions regarding the layout of the subsea production control system.