Purpose: To analyze the influence of perioperative complications in the management of biliary atresia (BA). Methods: A retrospective study was performed using a total of 422 BA patients who underwent Kasai portoenterostomy (KPE) in a single institution between February 2016 and May 2017. Data on patients' clinical characteristics, laboratory examinations, perioperative complications, and outcomes were collected. Unpaired two-tailed t-test and χ 2 test were employed for the comparison between BA patients with and without perioperative complications. Cox regression analysis was used to screen the risk factors for 2-years NLS in BA, and their influence on the 2-years NLS was analyzed using Kaplan-Meier survival analysis as well as the log-rank test. Results: The incidence of perioperative complications, 6-months jaundice clearance (JC) and 2-years native liver survival (NLS) rate were 60.4, 59.5, and 56.6%, respectively. Patients with perioperative complications had lower serum albumin (ALB) level, but higher aspartate aminotransferase-to-platelet ratio index (APRI) and international normalized ratio (INR) levels when compared with those without perioperative complications (ALB, P < 0.05; APRI, P < 0.01; INR, P < 0.05). Moreover, perioperative complications were correlated with glucocorticoid administration (P = 0.002). Univariate Cox regression analysis showed no relationship between perioperative complications and 2-years NLS (P > 0.05). However, multivariate Cox regression analysis indicated 6-months JC was an independent protective factor for 2-years NLS [P < 0.0001, hazard ratio (HR) = 0.074, 95% confidence interval = 0.05-0.11], and concordance index of this prediction model including age, weight, APRI, glucocorticoid, and 6-months JC was 0.811. Conclusion: Although perioperative complication is common during and after KPE, it had no influence on the prognosis of BA. However, assessment of the serum level of total bilirubin after KPE may serve as an important predictor for the outcome in BA.