Polyetheretherketone (PEEK) has become increasingly popular in dentistry and orthopedics due to its excellent chemical stability, reliable biosafety, and low elastic modulus. However, PEEK's biomechanical strength and bioactivity are limited and need to be increased as an implant material. The previous study in vitro has shown that the amino-functionalized carbon fiber reinforced PEEK (A-30%-CPEEK) possessed enhanced mechanical property and bioactivity. This study aims to evaluate the effect of amino groups modification on the osseointegration behavior of carbon fiber reinforced PEEK (30%-CPEEK) in rabbits. Herein, 30%-CPEEK and A-30%-CPEEK implant discs were implanted in rabbit skulls for 5 weeks, with pure titanium implants serving as a control. The bone-forming ability and osseointegration in vivo were systematically investigated by micro-computed tomography analysis, scanning electron microscope observation, and histological evaluation. Our results showed that all detection parameters were significantly different between the A-30%-CPEEK and 30%-CPEEK groups, favoring those in the A-30%-CPEEK, whose appraisal parameters were equal to or better than pure titanium. Therefore, this study supported the importance of amino groups in facilitating the new bone formation and bone-implant integration, suggesting that A-30%-CPEEK with enhanced osseointegration will be a promising material for dental or orthopedic implants.