Hypersonic vehicles emit strong infrared radiation from their high-temperature exhaust plume and body, which is critical for infrared early warning, tracking, and guidance. In this work, a comprehensive analysis is conducted on the factors involved in air dissociation reaction within the shock layer of hypersonic missile heads, as well as the multi-component afterburning effect of the exhaust plume. A novel Reverse Monte Carlo Method (RMCM) is proposed for infrared radiation calculation, which utilizes two-dimensional Low-Discrepancy Sequences (LDS) to improve computational accuracy. The numerical calculations for a dagger-type missile show that afterburning reactions increase the temperature on the centerline of the outlet exhaust plume by about 1000 K. The total infrared radiation intensity of the missile is the highest in the 1–3 μm band, with the high-temperature wall of the nozzle being the primary source of solid radiation, and gas radiation primarily coming from H2O. The radiation intensity of the missile exhaust plume in the 3–5 μm band is the highest, with radiation sources primarily coming from CO2, CO, and HCl. Afterburning reactions of the exhaust plume increase the total infrared radiation intensity of the missile by about 0.7 times. These results can provide reference for the detection and guidance of hypersonic missiles.