Polyether ether ketone (PEEK) has received much attention for its excellent mechanical properties and biocompatibility. Here, the silane coupling agent KH560 [γ-(2,3-epoxypropoxy)propyltrimethoxysilane] is used for graft modification of bioactive HA (hydroxyapatite) particles and for preparing HA/PEEK composites via a hot-press molding method. The prepared HA/PEEK composites were tested for their mechanical properties with SEM (scanning electron microscopy), infrared spectroscopy, and thermo-analysis. The results show that silane coupling KH-560 modifies HA successfully and that the tensile strengths of HA/PEEK and m-HA/PEEK composites indicate an increasing and then a decreasing tendency with increasing HA contents. The non-modified HA/PEEK composites display the same trend as the modified specimens with lower tensile strength and consist of sharp points. When the HA content is 5wt.%, the tensile strength of m-HA/PEEK composite reaches its maximum, which is 23% higher than that of pure PEEK specimens. The in vivo experiments of m-HA/PEEK used a biomechanical push-out test, SEM, optical microscopy, and an Image-Pro Express C image analysis system. The growth of the bone tissues around the m-HA/PEEK composites with an HA content of 5wt.% is better than that of specimens with different HA contents. This finding shows the nano-scale effect of the bioactive filler HA in PEEK substrates, which obviously contributes to the growth of the surrounding bone issues in vivo. This study could provide theoretical support for the further promotion and application of high-performance engineering plastics such as PEEK in biomedical fields.