Mitochondria are the energy source for basal cell functions as well as for tissue repair and regeneration. Excessive accumulation of reactive oxygen species (ROS) generated by bone tissue injury can cause cell oxidative stress and mitochondrial damage, negatively affecting osteogenic differentiation and tissue repair. However, efficient scavenging of mitochondrial ROS (mtROS) and restoration of mitochondrial homeostasis remain challenging. In this study, mitochondria‐targeted polyphenol/amino acid assembled nanoparticles (denoted as EC NPs) are constructed, which can achieve efficient intracellular ROS scavenging, especially for mtROS, recover the mitochondrial membrane potential, and enhance the inherent antioxidant system by increasing the antioxidase activity and GSH levels, following the re‐establishment of redox homeostasis. The EC NPs promoted AMPK‐mediated mitochondrial biogenesis, thereby providing more energy for osteogenic differentiation. Furthermore, the EC NPs not only recovered the osteogenic potential of the stem cells under oxidative stress but also demonstrated the ability to directly promote osteogenic differentiation by activating the cGMP‐PKG signaling pathway. In vivo experiments showed that the EC NPs significantly enhanced mitochondrial biogenesis and facilitated bone regeneration with a higher bone mass and bone mineral density. Thus, this multifunctional mitochondria‐targeted nanosystem represents a promising therapeutic strategy for bone regeneration based on mitochondrial homeostasis regulation.