Objective This study evaluates the prognostic significance of biochemical markers in diagnosing biliary fistulas (BF) in liver echinococcosis (LE). Methods The study included 85 patients with LE who underwent surgery between 2021 and 2024. Among them, 24 had BF (11 men, 13 women, mean age 40.5±14), and 61 had no BF (27 men, 34 women, mean age 38±13.4). Cysts were classified by WHO-IWGE criteria. Biochemical markers (total and conjugated bilirubin, ALP, GGT, ALT, AST, leukocyte count, eosinophils) were analyzed in blood and cyst contents. Statistical analysis used independent t-tests (p<0.05). Results Preoperative blood analysis showed no significant differences in bilirubin, ALP, GGT, ALT, AST, or leukocyte count between groups (p>0.05). However, eosinophil levels were significantly higher in the BF group (5.8±3.8% vs. 3.7±2.9%, p=0.0184). Cyst content analysis revealed significantly higher total bilirubin in BF cysts (28.8±21.4 µmol/L) versus non-BF cysts (1.2±0.9 µmol/L, p=0.00002). Conjugated bilirubin was also higher (16±15.3 µmol/L vs. 0.1±0.3 µmol/L, p=0.00018), while ALP and GGT showed no significant differences (p>0.05). Subgroup analysis (CE1-2 vs. CE3) showed no significant differences in biochemical markers between BF and non-BF groups (p>0.05), except eosinophils, which were higher in the BF group (p=0.0080). In CE1-2, occult BF cysts had higher total bilirubin than non-BF cysts (6±3.7 µmol/L vs. 1.2±1 µmol/L, p=0.0132). In CE3, total bilirubin was also significantly higher in BF cysts (p=0.00002). Further analysis showed that total bilirubin in obvious BF was 41±15.9 µmol/L, significantly higher than in occult BF (6±3.7 µmol/L, p<0.00001). Conclusion Biochemical analysis of cyst contents is superior to blood markers for BF verification. Total bilirubin in cyst contents had 100% specificity and 92.0% accuracy, with sensitivity increasing from 60.0% to 95% at a threshold of 2.6 µmol/L. Blood markers, including bilirubin and GGT, had limited diagnostic value. Elevated eosinophils (p=0.0184) were the only significant blood marker but lacked sufficient sensitivity (58.3%) and specificity (72.1%) for reliable preoperative diagnosis.