<p>Neuronal polarization is essential for functional compartmentalization, enabling dendritic synaptic integration and axonal action potential generation. Although structural differences in mitochondria across compartments have been identified, their functional distinctions remain unclear. Here, we uncovered compartment-specific mitochondrial Ca²⁺ dynamics and their molecular determinants. In axonal mitochondria, Ca²⁺ uptake through mitochondrial Ca²⁺ uniporter occurs independently of ER-stored Ca²⁺ release, with faster matrix Ca²⁺ clearance than dendritic mitochondria, where Ca²⁺ uptake predominantly originates from ER Ca²⁺. The ER-independent mitochondrial Ca²⁺ uptake in axonal mitochondria is associated with enriched mitochondrial Ca²⁺ uniporter-regulating proteins, MICU1 and MICU2, whereas higher NCLX expression facilitates rapid Ca²⁺ clearance. Moreover, NCLX knockdown, which functionally mimics a mental retardation-associated mutation, caused more significant developmental defects of axons than dendrites in vivo, aligning with its enrichment in axons. These findings highlight fundamental Ca²⁺-modulating features and developmental importance of neuronal mitochondria in a compartment-specific manner and reveal the key underlying molecular determinants.</p>