To improve the infrared stealth performance of the engine, an infrared characteristics real-time prediction model suitable for the overall design/control system simulation of small bypass ratio turbofan engine with typical exhaust system structure was developed. First, the accuracy and calculation speed of the model was proved to meet the requirements after comparing with CFD results; Then, the influence of the cycle parameters on the infrared characteristics was analyzed by the model. Steady-state numerical simulations were carried out for different flight missions, and the variation law of the engine infrared characteristics in the flight envelope was obtained. Finally, the dynamic response of infrared characteristics in transient state was studied. The results show that the infrared radiation intensity in the afterburner state increased by 1–2 orders of magnitude compared with the cruise state; The response speed of lateral infrared radiation intensity was basically consistent with that of thrust, while the response of backward infrared radiation intensity lagged greatly. Some useful implications from this study include turbofan overall optimized design and performance seeking control.