Background: Biliary atresia (BA) is the most common cause of cholestatic cirrhosis in children, and liver transplantation (LT) is the sole treatment for this disease. However, a young age and light weight increase the difficulty and risk of LT. Currently, Kasai portoenterostomy (KPE) is the preferred treatment for children with BA to buy time while waiting for a donor liver to become available. The pretransplant nutritional status is the key factor determining post-surgery quality of survival. Therefore, in this study, we followed 40 children with BA who survived with autologous livers after KPE from 2010 to 2017. Individualized nutritional guidance was given, and the post-KPE nutritional status of the children and the jaundice clearance rate were evaluated to better formulate follow-up and nutritional intervention strategies. Methods: The multidisciplinary team (MDT) carried out regular physical examinations of the children after KPE and supplemented them with a physiological dose of vitamin D (400–800 IU). In addition to feeding guidance, children with malnutrition were given medium-chain triglyceride (MCT)-enriched nutritional formula milk. The children’s body weights, body lengths, head circumferences, liver functions, bilirubin levels and plasma vitamin A, D and E levels were measured. The Z-score of physique and the percentiles were calculated using the anthropometric calculator of the WHO Anthro software, and descriptive statistics were evaluated. An independent-samples t-test was used to compare pre- and post-KPE indicators and vitamins. Results: A total of 40 children were included in the study. Their jaundice clearance rate was 56% within 3 months after KPE. Among them, 25 children had good compliance and were followed up at least twice. The patient ages at the last follow-up were 13.38±21.70 months. The male-to-female ratio was 24:16. The mean Z-score and percentiles of body weight and body length/height at the last follow-up for the 40 children were weight for age (WFA) (−1.49±1.54, 26.53±25.91) and length for age (LFA) (−1.39±1.16, 18.93±18.96, respectively). A total of 17.5% (7/40) of the children were emaciated, and 22.5% (9/40) had a short stature. The vitamin A, D and E levels were 0.99±0.29 µmol/L (marginal level), 34.12±16.71 µmol/L and 12.82±1.53 µg/mL, respectively, which did not differ compared to those of children of the same ages from the outpatient children’s health clinic. The prealbumin level was 150.82±47.48 mg/L (lower than the normal level), and the albumin level was 40.67±4.76 g/L (normal range). Conclusions: The jaundice clearance rate was 56% (14/25) for this group of children with BA within 3 months after KPE. At the last follow-up (13.38±21.70 months), the emaciation rate was approximately 17.5% (7/40), and the short stature rate was 22.5% (9/40), which reflected more prominent long-term malnutrition among the BA children. Multidisciplinary cooperation is very important for long-term nutrition management of BA children after KPE.