Synchrotron X-ray bioimaging was successfully carried out to observe bone regeneration by a novel artificial bone substitute of bioactive MegaGen Synthetic Bone (MGSB) and hyaluronate (HA) hydrogels. A biphasic calcium phosphate of MGSB was prepared by chemical precipitation method, with a porous spherical morphology. On the basis of the fact that HA plays important roles in bone regeneration and promotes the differentiation, vascularization, and migration of stem cells, HA-cystamine (CYS) hydrogels with cleavable disulfide linkages were prepared to supply HA continuously for effective bone regeneration by their controlled degradation in vivo. Among seven different samples using Bio-OSS®, MGSB, and/or several kinds of HA hydrogels, MGSB/HA-CYS hydrogels resulted in the most significant bone regeneration in the calvarial critical bone defect of New Zealand white rabbits. Histological and histomorphometric analyses revealed that the bone regeneration by MGSB/HA-CYS hydrogels was as high as 43%, occupying 71% of the bone defect area with MGSB in the form of a calvarial bone plate in 4 weeks. After that, MGSB was bioabsorbed and replaced gradually with regenerated bones as observed in 8 weeks. Synchrotron X-ray imaging clearly confirmed the effective bone regeneration by MGSB/HA-CYS hydrogels, showing three-dimensional micron-scale morphologies of regenerated bones interconnected with MGSB. In addition, sequential nondestructive synchrotron X-ray tomographic analysis results from anterior to posterior of the samples were well matched with the histomorphometric analysis results. The clinically feasible artificial bone substitutes of MGSB/HA-CYS hydrogels will be investigated further for various bone tissue engineering applications using the synchrotron X-ray bioimaging systems.