Hybrid manufacturing can enable rapid production of personalized artificial bones that are made of Polyether-ether-ketone (PEEK) by integrating 3D printing and milling. A main challenge, however, is the thermal stress deformation that arises from the fused deposition process, leading to warping and shrinkage. As a result, the fabrication accuracy is significantly diminished. This work aims to address this challenge by investigating the thermal stress deformation behavior of PEEK in hybrid manufacturing. The main contributions of this work, therefore, include the development of a model for this thermal deformation behavior, and the identification of key parameters such as cross-section length ( Ls), printed layer thickness ( Lh), and current workpiece height ( He). Further, experiments are conducted based on response surface methodology (RSM) to explore the relationships between temperature variation rate (Δ T), end surface height difference (Δ S), and length shrinkage rate (Δ L) with critical hybrid processing parameters. Optimal parameter combinations are then identified. Our experiments demonstrate that the proposed methods effectively reduce the effects of warping and shrinkage.