The dynamic interaction between the mitochondrial inner membrane (IM) and mitochondrial DNA (mtDNA) remains elusive due to the limitations in spatiotemporal resolution offered by conventional microscopy and the absence of suitable in vivo probes specifically targeting the IM. Here, we have developed a novel fluorescence probe called IMMBright660, characterized by exceptional photostability, fluorogenicity within lipid membranes, and low saturation power. Leveraging these features, we successfully employed time-lapse stimulated emission depletion microscopy (STED) at low power to visualize the IM, despite that mitochondria is highly photo-sensitive. By utilizing dual-color imaging of the IM and mtDNA, we have uncovered that mtDNA tends to habitat at mitochondrial tips or branch points, exhibiting an overall spatially uniform distribution. Notably, the dynamics of mitochondria are intricately associated with the positioning of mtDNA, and mitochondrial fusion consistently occurs in close proximity to mtDNA to minimize pressure during cristae remodeling. In healthy cells, >66% of the the mitochondria are Class III (with lengths longer than 5 μm or more than 12 cristae), while it dropped to <18% in ferroptosis. Mitochondrial dynamics, orchestrated by cristae remodeling, foster the even distribution of mtDNA. Conversely, in conditions of apoptosis and ferroptosis where the cristae structure is compromised, mtDNA distribution becomes irregular. These findings, achieved with unprecedented spatiotemporal resolution, reveal the intricate interplay between cristae and mtDNA and provide insights into the driving forces behind mtDNA distribution and expansion.