Introduction: This study aimed to investigate whether activating the Nrf2/TFAM pathway boosts mitochondrial biogenesis, reduces ferroptosis in ischemic stroke (IS), and evaluates Naotaifang (NTF) formula's therapeutic potential. Methods: Ferroptosis and mitochondrial biogenesis indicators were measured at various time points following MCAO. Various methods, including transmission electron microscopy, immunofluorescence assay, enzyme-linked immunosorbent assay, Western blotting assays, and real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR), were employed to evaluate the impact of NTF on mitochondrial biogenesis and ferroptosis in vivo and in vitro. Results: IS significantly inhibits mitochondrial biogenesis and increases neuronal ferroptosis, with brain damage worsening over time. MCAO groups showed reduced expression of Nrf2, TFAM, ATP, CISD2, FPN, GPX4, SOD, and HO-1, alongside elevated Fe²⁺, ROS, and LPO (P < 0.05) compared to the control group. Both sulforaphane and NTF treatment reversed these effects; NTF treatment effectively increased the expression of Nrf2, TFAM, FtMt, CISD1, CISD2, FPN, and GPX4 while inhibiting the levels of Fe2+, ROS, and LPO. (P < 0.05). Discussion: This finding clarifies mitochondrial biogenesis's crucial role, proposes a new "pathway + molecule" strategy for IS treatment, and supports NTF's clinical potential, though larger animal models and long-term safety studies are needed. Conclusion: In the context of IS, reduced mitochondrial biogenesis plays an important role in ferroptosis. Targeting the Nrf2/TFAM signaling pathway may improve mitochondrial biogenesis in IS. Furthermore, NTF can mitigate ferroptosis by promoting mitochondrial biogenesis through the Nrf2/TFAM signaling pathway