Excessive or chronic social stress induces emotional and cognitive disturbances and is a risk for mental illness. Reduced neuronal activity in the medial prefrontal cortex (mPFC) underlies these behavioral abnormalities. However, the subcellular origin and process of this neuronal change remain elusive. Here we examined ultrastructural alterations of mPFC neurons after social defeat stress in mice by serial electron microscopy and expansion microscopy. Social stress caused the loss of dendritic branches as well as morphological abnormality of subcellular structures, including mitochondria in remaining dendrites with varicosity-like membrane deformation. Social stress induced synaptic shrinkage selectively at mitochondria-containing synapses. Furthermore, multi-omics and functional analyses revealed that social stress deteriorated mitochondrial functions with decreased mitochondrial proteins at synapses. Pharmacological manipulation targeting mitochondria attenuated the synaptic shrinkage and depression-related behaviors. Together, these findings illustrate the importance of synaptic subcellular organelle in the synaptic pathology underlying stress and depression.