Objective The aim of this study is to investigate the instruction value of the serum cystatin C (Cys C) level monitoring for intervention opportunity of continuous blood purification technology (CBP) in children with severe sepsis. Methods 67 children with severe sepsis in the pediatric intensive care unit (PICU) with CBP treatment were retrospectively selected from May 2016 to April 2020. According to the time intervals between the time point of serum Cys C level began to increase (>15 mg/L) and the time point of CBP began, all children were divided into group A (<24 h, 29 cases), group B (24–48 h, 22 cases), and group C (>48 h, 16 cases). The children's general characteristics, vital signs, biochemical parameters, acute physiology and chronic health evaluation (APACHE II), and sequential organ failure assessment (SOFA) scores were evaluated. The influence factors of prognosis of children with severe sepsis were analyzed by multivariate regression analysis. Results The intervals between the time point of PICU hospitalization and the time point of CBP began and the times of CBP in group A were significantly more than those in group B and C (P < 0.05). There was no statistically significant duration of CBP among three groups (P > 0.05). After follow-up of 28 d, there was no significant difference on the occurrence of coagulation disorders and hypovolemic shock induced by CBP among three groups (P > 0.05). However, the mortality of children in group A was lower than that in group C (P < 0.05). Children in group A had lower APACHE II scores, SOFA scores, serum K+, blood urea nitrogen (BUN), serum creatine (SCr), partial pressure of carbon dioxide (PCO2), and higher partial pressure of oxygen (PO2) than those of children in group C after CBP. (P < 0.05). SOFA scores ≥5 after CBP treatment and the time intervals between the time point of serum Cys C level began to increase (>15 mg/L) and the time point of CBP began ≥24 h were the independent influence factors on the prognosis by multivariate regression analysis. Conclusion There are significant evidences that continuous blood purification technology within 24 h of serum Cys C level may better control the condition of children with severe sepsis.