Wound repair of bone is a complicated multistep process orchestrated by inflammation, angiogenesis, callus formation, and bone remodeling. Many bioactive factors (BFs) including cytokine and growth factors (GFs) have previously been reported to be involved in regulating wound healing of bone and some exogenous BFs such as bone morphogenetic proteins (BMPs) were proven to be helpful for improving bone healing. In this regard, the BFs reported for boosting bone repair were initially categorized according to their regulatory mechanisms. Thereafter, the challenges including short half-life, poor stability, and rapid enzyme degradation and deactivation for these exogenous BFs in bone healing are carefully outlined in this review. For these issues, BFs-imprinted scaffold vehicles have recently been reported to promote the stability of BFs and enhance their half-life in vivo. This review is focused on the incorporation of BFs into the modulated biomaterials with various forms of bone tissue engineering applications: firstly, rigid bone graft substitutes (BGSs) were used to imprint BFs for large scale bone defect repair; secondly, the soft sponge-like scaffold carrying BFs is discussed as filling materials for the cavity of bone defects; thirdly, various injectable vehicles including hydrogel, nanoparticles, and microspheres for the delivery of BFs were also introduced for irregular bone fracture repair. Meanwhile, the challenges for BFs-imprinted scaffold vehicles are also analyzed in this review.