Purpose Inpatients undergoing colonoscopy may be at increased risk of hypoglycemia. However, few high-quality studies have examined the relationship between hypoglycemia and colonoscopy in patients with type 2 diabetes mellitus (T2DM). Patients and Methods A total of 1016 patients from a large tertiary hospital were enrolled in this retrospective study. We collected demographic information, laboratory indices, colonoscopy information and hypoglycemia information from the enrolled patients during hospitalization. Logistic regression analysis was adopted to estimate the adjusted odds ratios to determine the association between hypoglycemia and colonoscopy. Results Hypoglycemia occurred in 80 of 788 (10.1%) patients without colonoscopy exposure and 37 of 228 (16.2%) patients with colonoscopy exposure. 25 patients (67.6%) had hypoglycemic events from 3 hours to 68 hours after the end of colonoscopy. Adjusting for demographic and clinical covariates, the risk of hypoglycemia was 1.99 times higher in those who underwent colonoscopy than in those who did not (OR 1.99, 95% CI 1.25–3.19). The association was consistent in subgroups of females, the elderly, the overweight patients, patients with long duration of disease or patients with suboptimal glycemic control. Conclusion A strong association between colonoscopy and an increased risk of hypoglycemia is observed in patients with T2DM. When performing a colonoscopy for diabetics, the risk of hypoglycemia should be considered even within 68 hours after colonoscopy.