A combined experimental and micromechanics investigation is conducted on elevated-temperature thermal expansion of PTFE/PEEK polymer-matrix composite reinforced with randomly oriented short carbon fibers (CF) and graphite flakes (Gr). In the experimental phase of the study, PTFE/PEEK polymer blends with different amounts of PTFE and four-phase CF/Gr/PTFE/PEEK composites with different volume fractions of graphite flakes were made from compression molding. Scanning electron microscopy was performed to evaluate the microstructure of the PTFE/PEEK matrix and the composite, especially the interface, and the size and dispersion of the particles. X-ray diffraction (XRD) was conducted to provide morphological information on the semi-crystalline PTFE/PEEK matrix of the composite. Differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) were carried out to determine transition temperatures and thermomechanical properties of the composite and its constituent phases at the elevated temperature. Thermal expansions of neat PTFE and neat PEEK, the PTFE/PEEK polymer matrix, and the CF/Gr/PTFE/PEEK composite were obtained with a thermal–mechanical analyzer (TMA) in a dilatometric mode. Coefficients of thermal expansion (CTEs) of the PTFE/PEEK matrix and its CF/Gr/PTFE/PEEK composite were then determined from 25 °C up to an elevated temperature 240 °C. To augment the experimental study, micromechanics analyses are also conducted to determine thermal expansion coefficients of the PTFE/PEEK matrix and the CF/GR/PTFE/PEEK composite. The micromechanics solutions elucidate individual roles of different composite constituents, contributions of individual constituent materials’ temperature-dependent thermal and mechanical properties, the importance of composite microstructure and morphology, and the issue of thermal–mechanical coupling on the thermal expansion behavior of the complex CF/Gr/PTFE/PEEK composite at high temperature.