Tooth root development is a complex process essential for tooth function, yet the role of root dentin development in tooth morphogenesis is not fully understood. Optineurin (OPTN), linked to bone disorders like Paget's disease of bone (PDB), may affect tooth root development. In this study, we used single-cell sequencing of embryonic day 16.5 (E16.5), postnatal day 1 (P1), and P7 mouse teeth, as well as embryonic and adult human teeth, to show that OPTN is vital for odontoblastic differentiation. In Optn mice, we observed short root deformities and defective dentin, with impaired apical papilla differentiation and increased apoptosis. In vitro OPTN downregulation in stem cells of the apical papilla (SCAPs) exacerbated apoptosis and hindered odontoblastic differentiation. RNA-seq analysis revealed significant differences in mitochondrial dynamics between control and OPTN knockout SCAPs. We discovered that OPTN influences mitochondrial dynamics primarily by promoting fission, leading to odontoblastic differentiation and mineralisation. Mechanistically, OPTN cooperates with NRF2 to regulate mitochondrial fission via DRP1 phosphorylation and affects the transcription of BCL2. Rescue experiments using an activator of NRF2 in ex vivo organ cultures and local gingival injection experiments confirmed these findings. Therefore, we concluded that OPTN, interacting with NRF2, acts as a key regulator of SCAPs mitochondrial dynamics, mineralisation and apoptosis during tooth development. These findings provide fresh insights into the mechanisms underlying tooth root development.