To improve the computational efficiency of multi-fidelity simulation, an improved fully coupled method was proposed, which was applied to the coupled simulation of a 3-D model of an exhaust system and a 0-D model of a turbofan engine. Different from conventional approach, by “truncating” the engine model, the CFD calculation of the exhaust system can be decoupled from the solution of nonlinear equations in the engine model, and an outer iteration equation set was constructed to solve the multi-fidelity model. It was found that the improved fully coupled method has better computational efficiency than traditional methods while maintaining equivalent computational results. Then, the improved fully coupled method was applied to the design of the central cone film cooling system, the influence of cooling gas bleed mechanism, the hole open area ratio of the central cone and hole density, hole direction, hole shape on the infrared characteristics was investigated. The impact of central cone film cooling on the overall performance of the engine was quantitatively evaluated. Combined with various favorable factors, when maintaining the HP rotor speed unchanged, the integrated infrared radiation intensity of the central cone under supersonic cruise conditions is reduced by 93% compared to the uncooled state, while the engine thrust increases by 0.3% and fuel consumption rate increases by 0.18%. The multi-fidelity simulation method proposed in this paper and the conclusions obtained are of great significance for the structural design of low-infrared exhaust systems.