Background: The clinical use of serum creatine (sCr) and cystatin C (CysC) in kidney function evaluation of critically ill patients has been in continuous discussion. The difference between estimated glomerular filtration rate calculated by sCr (eGFRcr) and CysC (eGFRcysc) of critically ill COVID-19 patients were investigated in this study. Methods: This is a retrospective, single-center study of critically ill patients with COVID-19 admitted in intensive care unit (ICU) at Wuhan, China. Control cases were moderate COVID-19 patients matched in age and sex at a ratio of 1:1. The eGFRcr and eGFRcysc were compared. The association between eGFR and death were analyzed in critically ill cases. The potential factors influencing the divergence between eGFRcr and eGFRcysc were explored. Results: A total of 76 critically ill COVID-19 patients were concluded. The mean age was 64.5 ± 9.3 years. The eGFRcr (85.45 (IQR 60.58-99.23) ml/min/1.73m 2 ) were much higher than eGFRcysc (60.6 (IQR 34.75-79.06) ml/min/1.73m 2 ) at ICU admission. About 50 % of them showed eGFRcysc < 60 ml/min/1.73 m 2 while 25% showed eGFRcr < 60 ml/min/1.73 m 2 (v 2 ¼ 10.133, p ¼ 0.001). This divergence was not observed in moderate group. The potential factors influencing the divergence included serum interleukin-6 (IL-6), tumor necrosis factor (TNF-a) level as well as APACHEII, SOFA scores. Reduced eGFRcr (<60 mL/min/1.73 m 2 ) was associated with death (HR ¼ 1.939, 95%CI 1.078-3.489, p ¼ 0.027). Conclusions: The eGFRcr was generally higher than eGFRcysc in critically ill COVID-19 cases with severe inflammatory state. The divergence might be affected by inflammatory condition and illness severity. Reduced eGFRcr predicted in-hospital death. In these patients, we advocate for caution when using eGFRcysc.