Fused deposition modeling (FDM) provides a promising technique for the small-batch fabrication of highly customized objects. The required performance of FDM far exceeds the performances of conventional manufacturing methods. However, the temperature difference that occurs during FDM generates internal stress, which causes warp deformation and affects formed sample quality. Hence, identifying the influencing factors of warp deformation is the key to improving the forming quality of FDM samples. In this work, PEEK/short carbon fiber (CF) composites were prepared by using the FDM method, the warp deformation formula was derived, and the warp deformation mechanism was obtained. Results showed that the material linear expansion coefficient, forming chamber temperature, and forming size had considerable effects on warp deformation. Moreover, CF could improve the warp deformation of the PEEK/CF composites because of their low Poisson’s ratio and high thermal conductivity. The addition of CF could reduce the residual stress of the composites and improve warp deformation. In addition, annealing could improve the tensile and bending mechanical properties of the PEEK/CF composites. Specifically, after 3 h of heat treatment at 190 °C, the tensile and bending mechanical properties of the composites reached 10.7% and 11.6%, respectively. Crystallinity analysis revealed that the mechanical properties of the PEEK/CF composites strongly depended on their crystallinity. High cooling temperature rates were associated with low crystallinity, tensile strengths, and elastic moduli. DMA analysis showed that the addition of CF could improve the high-temperature resistance of the PEEK/CF composites as reflected by the higher glass transition temperature of the composites than that of the pure PEEK resin. Porosity analysis showed that the CF content could tailor the pore size and distribution. The study reported here provides a reference for improving the forming quality and mechanical properties of PEEK/CF composites fabricated through FDM.