To retrospectively assess the value of the combination of conventional ultrasound and shear-wave elastography (SWE) in evaluating the segmental heterogeneity of liver fibrosis in biliary atresia (BA) patients after Kasai portoenterostomy. A total of 35 BA patients with liver segmental deformation were enrolled. The segmental deformation was assessed by conventional ultrasound followed with SWE examinations for evaluating the liver stiffness. Liver biopsy was performed in 11 patients in the region of SWE measurement and liver fibrosis was assessed using the Metavir classification. Aminotransferase to platelet ratio index (APRI) was calculated for comparison. The correlations between serum biochemical tests with SWE values were evaluated. Spearman's rank coefficient test was performed to evaluate the correlation between variables. The SWE values of the biopsy segments had significant positive correlations with liver fibrosis severity (r = 0.828, p = 0.001), which was better than APRI (r = 0.366, p = 0.242). The levels of bilirubin and transaminase showed significant correlations with the SWE values at hypertrophic segments in all patients (r from 0.336 to 0.576, all p < 0.05). Awareness of the segmental heterogeneity of liver fibrosis evaluated by conventional ultrasound and SWE may assist in selecting an appropriate biopsy location and predicting postoperative surveillance for patients with BA.