Three-dimensional (3D) printing of decellularized extracellular matrix (ECM) has been achieved to ensure real physiological environments for tissue engineering. However, the limited source, biocompatibility, and biosafety of decellularized ECM are deficiencies in its large clinical use. Autogenous ECM is biocompatible, bioactive, and biosafe, making it an optimal choice for future clinical applications of 3D printing. Here, we developed a multi-level customized 3D printing (MLC-3DP) strategy applying autogenous bone matrix (Auto-BM). This MLC-3DP includes shape specificity (shape), material specificity (Auto-BM), and cell specificity (autogenous cells) for true patient-specific repairs. Auto-BM (skull flaps) is readily accessible for specific patients after craniectomy, providing sufficient autogenous materials for MLC-3DP. Under mild conditions of this strategy, human-scale 3D printed samples can be fabricated using bioactive micron-sized Auto-BM particles. Multi-level customized autogenous bones (MLC-Auto-Bones) are finally obtained by combining autogenous bone marrow-derived mesenchymal stem cells (Auto-BMSCs). With autogenous materials and cells, MLC-Auto-Bones are inherently biocompatible and biosafe, providing good bioactivity for osteogenesis. In this implant, Auto-BMSCs can spontaneously differentiate into osteoblasts in vitro without additional osteogenic factors. In critical-sized skull defect models in vivo (3 months), implants integrate tightly to the defects' margin, facilitate mineralization, and generate vascularized mature bone. This work provides not only feasibility for patient-specific implants for skull defects, but also potential patient-specific solutions for other similar clinical requirements.