As the integration of devices in electronics manufacturing increases, there is a growing demand for thermal interface materials (TIMs) with high through-plane thermal conductivity. Vertically aligned carbon fiber (CF) thermally conductive composites have received considerable attention from researchers. However, the presence of significant interfacial thermal resistance at the interface between CFs and polymer presented a significant challenge to achieving the desired thermal conductivity, even in highly vertically aligned structures. Here, in addition to developing a polymer-based thermally conductive composite based on highly oriented CFs, we employed the Diels–Alder reaction to enhance the interfacial bonding between the CFs and the polymer matrix. Notably, we proposed the thermal conductivity enhancing mechanism of the highly oriented CFs filled silicone rubber (SR) composite originated from the strengthened interfacial bonding. The results indicated that the Diels–Alder reaction facilitated an increase in the thermal conductivity of the composite from 17.69 Wm− 1 K− 1 to 21.50 Wm− 1 K− 1 with a CF loading of 71.4 wt%. Additionally, a novel nano-indentation test was employed to analyse the interfacial strengthening of composites. Our research have significant implications for the advancement of thermal management in the field of electronics and energy, particularly with regard to the development of high-performance thermally conductive composites.