Individualized biological hydroxyapatite (BHA) scaffolds are essential for repairing critical craniomaxillofacial bone defects. Additive manufacturing relies on synthetic hydroxyapatite and biomimetic structures, making the resulting scaffolds inferior to natural bone. A subtractive manufacturing solution is proposed to cut natural bone blocks and then sinter them into BHA scaffolds. However, BHA scaffolds with fragile mechanical performance, fail to maintain scaffold integrity, due to microcracks generated by loss of organics from extracellular matrix (ECM). To preserve natural structure and enhance mechanical properties, ECM-gelatin hydrogel (ECM-Gel) is utilized as a micron-level coating to smooth surface microcracks like a facial mask. ECM-Gel shows potential in regulating blood clot fibrin network which may induce a favorable macrophage-mediated bone regeneration. Therefore, a gelatin hydrogel-masked BHA (G-BHA) scaffold system is developed using crosslinker genipin (2 and 8 mM). ECM-Gel formed a “hybrid layer”, smoothing the micron-level microcracks and enhancing mechanical properties of BHA; it activated platelets to lock blood clot with dense fibrin network, inducing M2 macrophage via a potential endocytosis-macroautophagy-inflammation axis for bone regeneration. In vivo experiments confirmed G-BHA scaffolds promoted ectopic and in situ bone regeneration. Therefore, ECM-gel-masking demonstrates great potential in developing individualized bioauthentic bone scaffolds with favorable blood clot and macrophage-mediated bone regeneration.