Polyetheretherketone (PEEK), a high-performance special engineering plastic, has gradually been used in bone substitutes due to its wear resistance, acid and alkali resistance, non-toxicity, radiolucency, and modulus close to that of human bone. However, its stable biphenyl structure determines strong biological inertness, thus artificial interventions are required to improve the biological activity of fabricated PEEK parts for better clinical applications. This study developed a novel strategy for grafting bioactive glass (BAG) onto the surface of PEEK through sulfonation reaction with concentrated sulfuric acid (H2SO4), aiming to improve the bioactivity of printed porous bone scaffolds manufactured by fused deposition modeling (FDM) to meet clinical individual needs. In vitro biological study was conducted on sulfonated polyetheretherketone-bioactive glass (SPEEK-BAG) scaffolds obtained by this strategy. The results demonstrated that the optimal modification condition was a 4-hour sulfonation reaction with 1 mol/L concentrated H2SO4 at high temperature and high pressure. The scaffold obtained under this condition showed minimal cytotoxicity, and the Ca/P molar ratio, yield compressive strength, and compressive modulus of this scaffold were 2.94 ± 0.02, 62.78 MPa, and 0.186 GPa respectively. The hydrophilicity and the biomineralization ability of PEEK modified by the proposed strategy were substantially improved. The SPEEK-BAG bone scaffolds exhibited excellent biocompatible properties, suggesting that the sulfonation reaction and BAG effectively enhanced the proliferation and differentiation of osteoblasts. The presented method provides an innovative, highly effective, and customized strategy to improve the biocompatibility and bone repair ability of printed PEEK bone scaffolds for virous biomedical applications.