The thermal management system (TMS) for aircraft fuel is a critical component of integrated TMSs in aircraft. As such, its optimal design is necessary to ensure the efficient completion of flight missions. This study presents the model building of a numerical simulation model for the fuel TMS, with the objective of minimizing fuel return flow. Sensitivity analysis was performed using variance analysis. The genetic algorithm was utilized for the optimization of the model building, taking into consideration the system’s geometric structure and performance parameters, which include the pipe length, the ram air-fuel HX’s efficiency, and the ram air’s volume flow rate in the ram air cooling subsystem, as design variables. The optimization solution for system design variables yielded a design scheme with the highest working efficiency for the fuel TMS. In this paper, the genetic algorithm in AMEsim software is adopted, which can also effectively optimize the design parameters and achieve the optimization objective. Compared with the original TMS structure, the heat dissipation capacity of the fuel TMS is improved and reduced the return fuel flow by 67.4% after the optimization of system structure parameters.