Objective To explore the relationship between levels of serum cystatin C (Cys-C) and neutrophil gelatinase-associated lipocalin (NGAL) and severity and prognosis of acute kidney injury secondary to sepsis. Methods The clinical data of 95 patients with sepsis admitted to the hospital from October 2018 to October 2022 were retrospectively analyzed. According to the severity of secondary acute kidney injury, the patients were divided into mild group (n=21), moderate group (n=31) and severe group (n=43), and the differences in serum Cys-C and NGAL levels among the three groups were compared. The patients were classified into good prognosis group (n=67) and poor prognosis group (n=28) according to the prognosis, and the differences in serum Cys-C and NGAL levels were compared between the two groups. The correlation between serum Cys-C and NGAL levels and severity and prognosis of acute kidney injury secondary to sepsis was analyzed, and ROC curve was used to analyze the predictive efficiency of serum Cys-C and NGAL levels on prognosis of patients with acute kidney injury secondary to sepsis.Results The levels of serum Cys-C and NGAL in severe group were higher than those in moderate group and mild group (P＜0.05), and the above levels in moderate group were higher than those in mild group (P＜0.05). The levels of serum Cys-C and NGAL were lower in good prognosis group than those in poor prognosis group (P＜0.05). Serum Cys-C and NGAL levels were positively correlated with the severity of acute kidney injury secondary to sepsis (P＜0.05), and were negatively correlated with the prognosis of patients with acute kidney injury secondary to sepsis (P＜0.05). Serum Cys-C and NGAL had certain predictive efficiency on the prognosis of acute kidney injury secondary to sepsis (both AUC＞0.5), and the cut-off values were 9.32mg/L and 182.95ng/mL respectively. Conclusion Serum Cys-C and NGAL levels are related to the disease severity and prognosis of patients with acute kidney injury secondary to sepsis. The higher the levels of serum Cys-C and NGAL, the more serious the disease condition and the worse the prognosis. Clinical detection of serum Cys-C and NGAL levels can provide certain guidance for clinical treatment