Bioactive molecules have shown great promise for effectively regulating various bone formation processes, rendering them attractive therapeutics for bone regeneration. However, the widespread application of bioactive molecules is limited by their low accumulation and short half-lives in vivo. Hydrogels have emerged as ideal carriers to address these challenges, offering the potential to prolong retention times at lesion sites, extend half-lives in vivo and mitigate side effects, avoid burst release, and promote adsorption under physiological conditions. This review systematically summarizes the recent advances in the development of bioactive molecule-loaded hydrogels for bone regeneration, encompassing applications in cranial defect repair, femoral defect repair, periodontal bone regeneration, and bone regeneration with underlying diseases. Additionally, this review discusses the current strategies aimed at improving the release profiles of bioactive molecules through stimuli-responsive delivery, carrier-assisted delivery, and sequential delivery. Finally, this review elucidates the existing challenges and future directions of hydrogel encapsulated bioactive molecules in the field of bone regeneration.