Background Bile duct injury after ablation of malignant liver tumors (MLTs) was not unusual and should be avoided. However, few studies have focused on evaluating the risk factors for intrahepatic bile duct injury. Aim To evaluate the risk factors for intrahepatic bile duct injury after ablation of MLTs and to evaluate the minimum safe distance for ablating tumors abutting bile ducts. Methods Sixty-five patients with intrahepatic bile duct injury after ablation of MLTs, and 65 controls were recruited. Risk factors for intrahepatic bile duct injury were analyzed. Tumor location was recorded as ≤5 mm (group A), 5–10 mm (group B), and >10 mm (group C) from the right/left main duct or segmental bile duct. Results Ascites history ( P  < 0.001), TACE treatment history ( P  = 0.025), intrahepatic bile duct dilatation before ablation ( P  < 0.001), and tumor location ( P  = 0.000) were identified as significant risk factors for intrahepatic bile duct injury. Significant differences in the risk of intrahepatic bile duct injury were found between groups B and C ( P  = 0.000), but not between groups A and B ( P  = 0.751). Ascites history ( P  = 0.002) and tumor location ( P  < 0.001) were independent predictors with the OR (95 % confidence interval) of 39.31(3.95–391.69) and 16.56 (5.87–46.71), respectively. Conclusions Bile duct injury after ablation of MLTs was the result of local treatment-related factors combined with the patients’ general condition. The minimum safe distance for ablation of tumor abutting a bile duct was 10 mm.