Introduction: Methods: The optimal extraction process of Results: The optimal extraction conditions (80% ethanol, solid-liquid ratio of 1:20, 60 °C for 30 min) yielded a flavonoid content of 10.72%. The crude flavonoid extract exerted a significant concentration-dependent inhibitory effect on protoscoleces, with an inhibition rate of 85.88% at 40 mg/mL for 24 h. The extract severely damaged protoscolex ultrastructure and upregulated Caspase-3 activity by 4.22-fold to induce protoscolex apoptosis. Biosafety evaluation confirmed that 10 mg/mL flavonoids had no obvious host cell toxicity, with a mouse oral LD₅₀ of 1.43 g/kg and no pathological damage in major organs. In vivo results showed that 20 mg/kg flavonoid treatment effectively reduced hepatic cyst numbers and promoted fibrotic repair in mice. Multi-omics analysis identified 50 flavonoid components and 25 differentially expressed proteins enriched in antiviral immune and RNA degradation pathways, and 16 flavonoids with high target-binding affinity were screened. Among them, myricetrin was the only active monomer, and 5 mg/mL myricetrin glycoside treatment significantly reduced liver cyst volume and achieved effective parasite clearance and tissue repair in vivo. Discussion: This study systematically demonstrates the prominent anti-echinococcosis activity and good biosafety of B. javanica flavonoids both in vitro and in vivo. The flavonoids kill E. granulosus protoscoleces by destroying parasite structure and activating apoptotic pathways, and alleviate liver lesions by promoting tissue fibrosis repair. Myricetrin is identified as the core active substance responsible for the anti-parasitic effect. These findings reveal the material basis and potential mechanism of B. javanica against echinococcosis, filling the gap of natural anti-echinococcosis drug research. This work provides a reliable experimental basis for the development of novel safe and efficient anti-echinococcosis natural drugs, and offers a new strategy for the clinical treatment of cystic echinococcosis.