A combined experimental and theoretical investigation is conducted on elevated-temperature thermal transport properties of a multifunctional polytetrafluoroethylene (PTFE)/polyetheretherketone (PEEK) matrix composite containing short carbon fibers and graphite flakes. In experiments, X-ray diffraction (XRD), scanning electron microscope (SEM), and optical microscopy are used to determine morphologies and microstructure of neat PTFE and PEEK polymers, PTFE/PEEK blend, and individual PTFE and PEEK phases in the carbon fiber (CF)Gr/PTFE/PEEK composite. Microstructure parameters determined are used in subsequent analytical modeling and predictions. Effective heat capacity and thermal conductivities of the composite and its polymer matrix are determined by a modulated differential scanning calorimetry (MDSC) method with temperature up to 225 °C. The results show that thermal transport properties of the composite are significantly affected by temperature and polymer transitions. The carbon fibers and graphite in the composite improve its mechanical and tribological performance and also enhances heat conduction. Thermal diffusivity of the composite, however, is governed by the PTFE/PEEK matrix due to its high thermal capacity. In the theoretical/analytical study, thermodynamic considerations are made at both molecular and micromechanical levels. Theoretical models and micromechanics analyses are used to determine effective thermal transport properties of the composite. The results clarify the roles of individual constituents and temperature effects on the composite thermal transport. Thermal percolation predictions compare well with experimental data; they also reveal that 10% (by volume) graphite lubricant in the carbon fiber-reinforced PTFE/PEEK composite leads to formation of effective thermal conductive networks, which rapidly increases thermal percolation due to their high efficiency of thermal transport.