Aim of this study is to evaluate the differences in corneal endothelial cell morphology and corneal thickness in patients with and without type 2 diabetes related to age, disease duration, and HbA1c percentage. This retrospective cross-sectional study included 511 (1022 eyes) type 2 diabetes patients and 900 (1799 eyes) non-diabetic patients. The endothelial cell density (ECD), variation in endothelial cell size (CV), percentage of hexagonal cells, and central corneal thickness (CCT) were analyzed using a noncontact specular microscope and a Pentacam Scheimpflug camera. We also examined the correlation between the corneal parameters and the duration of diabetes. For total ages, the subjects with type 2 diabetes showed significantly lower ECD, hexagonality, higher CV, and thicker CCT than the control group. This difference was more pronounced in patients with long-standing DM (≥ 10 years) and high HbA1c (≥ 7%). When stratified by age group, from the 60 s group, corneal endothelial cell parameters showed a statistically significant difference between DM and control groups. The duration of diabetes was inversely correlated with ECD (r = - 0.167; p = 0.000). These findings suggest that diabetes affects corneal endothelial cell in older age and those with long-standing DM and higher HbA1c. Regular corneal endothelial examinations are required in diabetic patients.