Temporal lobe epilepsy (TLE) is the most common refractory subtype of epilepsy in clinical practice, with a complex pathogenesis and a lack of precise biomarkers for diagnosis and prognosis evaluation, seriously affecting the quality of life of patients. The hippocampus and amygdala, as the core structures of the limbic system, play a key role in the pathogenesis of TLE. Structural abnormalities in both are considered important pathological bases for the initiation, spread, and progression of epileptic discharges. Although conventional magnetic resonance imaging can detect obvious hippocampal sclerosis, it is difficult to capture microstructural changes and has limited ability to identify hidden damage in areas such as the amygdala, leading to misdiagnosis or missed diagnosis in some patients with hidden TLE. Voxel-based morphological analysis (VBM) can accurately quantify the volume and density changes of the whole brain gray and white matter, providing technical support for analyzing the microstructural damage of the hippocampus and amygdala in TLE patients. Previous studies have suggested that the amygdala is not only a “susceptible area” for epileptic discharges, but may also serve as a “relay station” involved in discharge diffusion. Its structural abnormalities are closely related to the frequency and prognosis of TLE attacks. However, the synergistic effect and specific pathological mechanisms of structural changes in the hippocampus and amygdala still need to be further clarified. Therefore, this study used VBM technology to systematically analyze the magnetic resonance imaging manifestations of the hippocampus and amygdala in TLE patients, aiming to reveal their structural abnormalities and provide imaging evidence for the accurate diagnosis, mechanism research, and prognosis evaluation of TLE.