Focal cortical dysplasia (FCD) is a developmental disorder of the cerebral cortex and a main cause of drug-resistant epilepsy in children. A loss of the excitation and inhibition (E/I) balance has emerged as a key feature for neuronal hyperexcitability, underlying the pathogenesis of seizures. However, it remains unclear how synaptic ultrastructure is altered in the human patients with FCD. Here we performed morphological analyses on the synaptic density, shape, and distribution of intrasynaptic organelles in the temporal cortical layer III of a FCD patient using 3D electron microscopy. Our quantitation showed a reduced density of symmetric (inhibitory) synapses in the soma of pyramidal neurons. Notably, we also found a reduction in asymmetric (excitatory) synapses in the dysplastic region compared to control. Further analyses of excitatory synapses revealed that there were extra-large synapses in the dysplastic region, with a concomitant increase in the number of synaptic vesicles. Moreover, the distance from inhibitory synapses to the nearest excitatory synapses along the dendrite was significantly lengthened in the dysplastic region, which would compromise effective inhibition over excitation. Additionally, the densities of both presynaptic boutons containing mitochondria and postsynaptic protrusions harboring a spine apparatus (SA) were decreased in the epileptogenic region, supporting defects in intracellular calcium buffering and synaptic plasticity. Finally, maladaptive myelination was prominent in the dysplastic region. Collectively, these disturbances of synaptic structures may represent pathogenetic mechanisms underlying the neuronal hyperexcitability of the human patient with FCD.