Various biocompatible and biodegradable scaffolds blended with biochemical signal molecules with adequate osteoinductive and osteoconductive properties have attracted significant interest in hard tissue engineering regeneration. We evaluated the distinct effects of magnesium borate, zinc borate, and boric acid blended into chitosan scaffold for osteogenic differentiation of stem cells from exfoliated deciduous teeth. Stem cells from exfoliated deciduous teeth cells are a potential source of functional osteoblasts for applications in bone tissue engineering, but the efficiency of osteoblastic differentiation is low, thereby significantly limiting their clinical applications. Divalent metal borates have potential function in bone remodeling because they can simulate bone formation and decrease bone resorption. These magnesium, zinc, and B ions can gradually be released into the culture medium from the scaffold and induce advanced osteoblastic differentiation from stem cells from exfoliated deciduous teeth. Stem cells from exfoliated deciduous teeth with magnesium borate or zinc borate as inducer demonstrated more osteoblastic differentiation after 21 days of culture. Differentiated cells exhibited activity of alkaline phosphatase, bone-related gene expression of collagen type I, runt-related transcription factor 2, osteopontin, osteocalcin, vascular endothelial growth factor, and angiopoietin-1, as noted via real-time polymerase chain reaction analysis, as well as significant deposits of calcium minerals. Divalent mental magnesium and zinc and nonmetal boron can be an effective inducer of osteogenesis for stem cells from exfoliated deciduous teeth. This experiment might provide useful inducers for osteoblastic differentiation of stem cells from exfoliated deciduous teeth for tissue engineering and bone repair.