Scaffold-free bone microtissues differentiated from mesenchymal stem cell (MSC) spheroids offer great potential for bottom-up bone tissue engineering as a direct supply of cells and osteogenic signals. Many biomaterials or biomolecules have been incorporated into bone microtissues to enhance their osteogenic abilities, but these materials are far from clinical approval. Here, we aimed to incorporate hydroxyapatite (HAP) nanoparticles, an essential component of bone matrix, into MSC spheroids to instruct their osteogenic differentiation into bone microtissues and further self-organization into bone organoids with a trabecular structure. Furthermore, the biological interaction between HAP nanoparticles and MSCs and the potential molecular mechanisms in the bone development of MSC spheroids were investigated by both in vitro and in vivo studies. As a result, improved cell viability and osteogenic abilities were observed for the MSC spheroids incorporated with HAP nanoparticles at a concentration of 30 μg/mL. HAP nanoparticles could promote the sequential expression of osteogenic markers (Runx2, Osterix, Sclerostin), promote the expression of bone matrix proteins (OPN, OCN, and Collagen I), promote the mineralization of the bone matrix, and thus promote the bone development of MSC spheroids. The differentiated bone microtissues could further self-organize into linear, lamellar, and spatial bone organoids with trabecular structures. More importantly, adding FAK or Akt inhibitors could decrease the level of HAP-induced osteogenic differentiation of bone microtissues. Finally, excellent new bone regeneration was achieved after injecting bone microtissues into cranial bone defect models, which could also be eliminated by the Akt inhibitor. In conclusion, HAP nanoparticles could promote the development of bone microtissues by promoting the osteogenic differentiation of MSCs and the formation and mineralization of the bone matrix via the FAK/Akt pathway. The bone microtissues could act as individual ossification centers and self-organize into macroscale bone organoids, and in this meaning, the bone microtissues could be called microscale bone organoids. Furthermore, the bone microtissues revealed excellent clinical perspectives for injectable cellular therapies for bone defects.