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Biomineralization of natural polymers in simulated body fluid (SBF) can significantly improve its biocompatibility, osteoconductivity, and osteoinductivity because of the hydroxyapatite (HAp) deposition. Nevertheless, the superficial HAp crystal deposition hamper the deep inorganic ions exchange in porous microgels, thus gradually leading to a nonuniform regeneration effect. Inspired by the pearl forming process, this article uses the microarray chips to fabricate the multi-layer mineralized graphene oxide (GO)-collagen (Col)-hydroxyapatite (HAp) microgel, denoted as MMGCH. These fabricated MMGCH microgels exhibit porous structure and uniform HAp distribution. Furthermore, the suitable microenvironment offered by microgel promotes the time-dependent proliferation and osteogenic differentiation of stem cells, which resulted in upregulated osteogenesis-related genes and proteins, such as alkaline phosphatase, osteocalcin, and collagen-1. Finally, the MMGCH microgels possess favorable bone regeneration capacities both in cranial bone defects and mandibular bone defects via providing a suitable microenvironment for host-derived cells to form new bone tissues. This work presents a biomimetic means aiming to achieve full-thickness and uniform HAp deposition in hydrogel for bone defect repair.