Objective To investigate the brain structural features of children with focal cortical dysplasia (FCD) misdiagnosed or missed by 3D high-resolution magnetic resonance imaging (MRI).Methods A retrospective analysis was performed for the MRI and pathological data of 23 children with FCD confirmed by postoperative pathology who were misdiagnosed or missed before surgery, and a postoperative depth analysis was used to identify the abnormal signs on MRI and the corresponding pathological morphology and features.Results Of all 23 children, 5 (21.74%) were found to have abnormal morphology of the local cerebral sulci, with negative results of preoperative reading; 7 (30.43%) had abnormal morphology of the local brain gyrus, among whom 3 had congenital dysplasia and 4 had negative results of preoperative reading; 4 (17.39%) had a reduction in the volume of local white matter and were diagnosed with delayed myelination before surgery; 2 (8.70%) had a slight increase in the local signal in white matter, among whom 1 was diagnosed with poor myelination and 1 had negative results of preoperative reading; 2 (8.70%) had segmental cerebral atrophy and were diagnosed with localized subarachnoid space enlargement based on preoperative reading; 3 (13.04%) were diagnosed with tuberous sclerosis before surgery. Pathological examination showed varying degrees of dysplasia, abnormal neurons, and cells with ballooning degeneration.Conclusions FCD in some children lack typical MRI signs, and slight structural abnormalities and atypical MRI signs can guide accurate preoperative evaluation and localization.