By installing an intercooler and a recuperator, the intercooled recuperative aero engine (IRA) has the advantage of improving thermal efficiency as well as reducing fuel consumption and emissions. Both the aerodynamic and thermal performance of the intercooler and recuperator, as well as their configuration have decisive effects on the performance of the engine. This paper first describes the overall parameters and the structural scheme for the IRA engine. Then numerical simulation and modeling tests were conducted to investigate the performance of different types of matrices for the intercooler. Results show that the cross-corrugated matrix, compared to the tube matrix, had higher effectiveness and lower pressure loss. For the recuperative system, which includes the matrix module and the pipe system, a porous medium model was established for the U-tube recuperator matrix according to the experimental results. With this model, the optimized arrangement of the eight recuperator modules in the exhaust nozzle was achieved. After optimization, the gas almost equally flows through each matrix module, which can ensure the heat transfer effectiveness as design. A flow network was built up to optimize the pipe system of the recuperator. With this network, the diameter of the pipes inside the air supply/backflow ducting system was optimized to make the coolant flow through each matrix module matching the gas side.