Objective: This study aimed to evaluate the effect of a femtosecond laser on the osteogenetic efficiency of polyetheretherketone (PEEK) and its composite for clinical applications. Methods: One hundred pieces of PEEK and its composite (6 × 4 × 2 mm3) were randomly divided into four groups and treated as follows: group A1, PEEK; group A2, PEEK + femtosecond laser; group B1, PEEK composite; and group B2, PEEK composite + femtosecond. The surface morphology of the pieces of each group was observed through scanning electron microscopy. The surface roughness and wettability, which were considered as the main parameters affecting cell adhesion characteristics of implants, were measured. The animals whose mandibles were implanted with the four groups of materials were killed at the end of 6 and 12 weeks. Various characterization tests, such as Cone Beam Computed Tomography (CBCT), push-out test, microscope test, and bone implant contact , were conducted to investigate the healing effect between materials and bones. Results: In group B1, the nanoparticles in PEEK were uniformly distributed. In groups A2 and B2, many periodic nanostructures were observed. The surface roughness and wettability of group B2 were significantly increased compared to those of the other groups ( p < 0.05). At each time point, the number of trabecular bones, contact strength, and BIC of group B2 were higher than those of the three other groups ( p < 0.05). Compared with those of group A1, the test results of group B1 were significantly improved. Conclusion: Femtosecond lasers can effectively enhance the biological activity of PEEK and its composite; PEEK composite exhibits better biological activity than PEEK.