Objective: To evaluate the diagnostic value of modified hepatobiliary scintigraphy in children with biliary atresia (BA) across varying degrees of liver injury. Methods: A retrospective analysis was conducted on 272 infants with persistent jaundice, including 113 cases of BA confirmed by follow-up or pathology and 159 cases of intrahepatic cholestasis. Based on ALBI scores, patients were divided into two groups: a mild-to-moderate liver injury group (n=212) and a severe liver injury group (n=60). A modified analytical approach, combining visual analysis within 6 hours with semi-quantitative assessment of bowel excretion delay, was applied as an improved method for hepatobiliary scintigraphy. The diagnostic efficacy of conventional hepatobiliary scintigraphy, the modified method, and ultrasound for BA was compared. Results: In the mild-to-moderate liver injury group, the modified hepatobiliary scintigraphy method demonstrated sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) of 96.88%, 95.69%, 96.23%, 94.90%, and 97.37%, respectively, for diagnosing BA. Compared with the conventional method, the modified approach showed significantly higher specificity, accuracy, and PPV (all P<0.01), while no significant differences were observed in sensitivity or NPV (all P>0.05). Compared with ultrasound, the modified method exhibited significantly higher sensitivity, accuracy, and NPV (all P<0.01), with no significant differences in specificity or PPV (all P>0.05). In the severe liver injury group, the modified method showed sensitivity, specificity, accuracy, PPV, and NPV of 88.24%, 88.37%, 88.33%, 75%, and 95%, respectively. Compared with the conventional method, the modified approach had significantly higher specificity, accuracy, and PPV (all P<0.01), while no significant differences were found in sensitivity or NPV (all P>0.05). There were no significant differences between ultrasound and the modified method across all metrics (all P>0.05). Conclusions: The modified hepatobiliary scintigraphy method offers high diagnostic value for children with BA across varying degrees of liver injury.