In this study, the adhesion strength between a low-emissivity Al/polysiloxane coating and the polyimide/carbon fiber substrate at high-temperatures was successfully enhanced. The surface microstructure, adhesion, thermal properties, and optical performance of the samples were measured by scanning electron microscopy, tensile testing, simultaneous thermal analysis, infrared spectroscopy, and infrared thermal imaging. The coating structural analysis results showed that the emissivity of the top of the coating was lower than that of the bottom owing to the high enrichment ratio of Al powder with good infrared reflectance on the top. The thermal stability of the polyimide/carbon fiber substrate was studied to explore the effects of high temperature on the substrate surface structure and composition. Moreover, the failure mechanism of the adhesion strength between the coatings and substrate was explained, and the adhesion strength after being heated at 500 °C for 30 min was successfully enhanced using a resin intermediate layer and thermal pre-treatment step. Substrate pre-treatment at 500 °C for 6 min increased the adhesion strength by 3.5 ± 0.4 MPa because of the polysiloxane resin intermediate layer. The adhesion strength increased from 0.5 ± 0.4 to 5.0 ± 0.4 MPa when the pre-treatment time of polyimide/carbon fiber increased from 0 to 6 min. The potential applications of carbon fiber on the infrared stealth and energy saving fields at high temperatures might be improved by adding high-temperature resistant low-emissivity organic coatings to reduce infrared absorption and radiation.