Background: This research aimed to delve into the cortical morphological transformations in patients with magnetic resonance imaging (MRI)-negative temporal lobe epilepsy (TLE-N), seeking to uncover the neuroimaging mechanisms behind these changes. Methods: A total of 29 individuals diagnosed with TLE-N and 30 healthy control participants matched by age and sex were selected for the study. Using the surface-based morphometry (SBM) technique, the study analyzed the three-dimensional-T1-weighted MRI scans of the participants' brains. Various cortical structure characteristics, such as thickness, surface area, volume, curvature, and sulcal depth, among other parameters, were measured. Results: When compared with the healthy control group, the TLE-N patients exhibited increased insular cortex thickness in both brain hemispheres. Additionally, there was a notable reduction in the curvature of the piriform cortex (PC) and the insular granular complex within the right hemisphere. In the left hemisphere, the volume of the secondary sensory cortex (OP1/SII) and the third visual area was significantly reduced in the TLE-N group. However, no significant differences were found between the groups regarding cortical surface area and sulcal depth (p < 0.025 for all, corrected by threshold-free cluster enhancement). Conclusions: The study's initial findings suggest subtle morphological changes in the cerebral cortex of TLE-N patients. The SBM technique proved effective in identifying brain regions impacted by epileptic activity. Understanding the microstructural morphology of the cerebral cortex offers insights into the pathophysiological mechanisms underlying TLE.