This study was designed to investigate the association between Charlson Comorbidity Index (CCI) and in-hospital mortality and other clinical outcomes among patients with hyperglycemic crises. This retrospective cohort study was conducted using data from electric medical records. A total of 1668 diabetic patients with hyperglycemic crises from six tertiary hospitals met the inclusion criteria. CCI < 4 was defined as low CCI and CCI ≥ 4 was defined as high CCI. Propensity score matching (PSM) with the 1:1 nearest neighbour matching method and the caliper value of 0.02 was used to match the baseline characteristics of patients with high CCI and low CCI to reduce the confounding bias. In-hospital mortality, ICU admission, hypoglycemia, hypokalemia, acute kidney injury, length of stay (LOS), and hospitalisation expense between low CCI and high CCI were compared and assessed. Univariate and multivariate regression were applied to estimate the impact of CCI on in-hospital and other clinical outcomes. One hundred twenty-one hyperglycemic crisis (HC) patients died with a mortality rate of 7.3%. After PSM, compared with low CCI, patients with high CCI suffered higher in-hospital mortality, ICU admission, LOS, and hospitalisation expenses. After multivariate regression, age (aOR: 1.12, 95% confidence interval [CI]: 1.06-1.18, p < 0.001), CCI(aOR: 4.42, 95% CI: 1.56-12.53, p = 0.005), uninsured (aOR: 22.32, 95% CI: 4.26-116.94, p < 0.001), shock (aOR: 10.57, 95% CI: 1.41-79.09, p = 0.022), mechanical ventilation (aOR: 75.29, 95% CI: 12.37-458.28, p < 0.001), and hypertension (aOR: 4.34, 95% CI: 1.37-13.82, p = 0.013) were independent risk factors of in-hospital mortality of HC patients. Besides, high CCI was an independent risk factor for higher ICU Admission (aOR: 5.91, 95% CI: 2.31-15.08, p < 0.001), hypoglycemia (aOR: 2.19, 95% CI:1.01-4.08, p = 0.049), longer LOS (aOR: 1.23, 95% CI: 1.19-2.27, p = 0.021), and higher hospitalisation expense (aOR: 2089.97, 95% CI: 193.33-3988.61, p = 0.031) of HC patients. CCI is associated with in-hospital mortality, ICU admission, hypoglycemia, LOS, and hospitalisation expense of HC patients. CCI could be an ideal indicator to identify, monitor, and manage chronic comorbidities among HC patients.