Baicalein, a natural flavonoid, is structurally advantageous for binding to xanthine oxidoreductase. In our study, molecular docking analysis and Surface Plasmon Resonance revealed a direct interaction between baicalein and xanthine oxidoreductase. Moreover, 50 mg/kg/d baicalein treatment significantly suppressed the viability of xanthine oxidoreductase in hyperuricemia mouse model. The data showed that baicalein remarkably prevented renal dysfunction, ameliorated kidney fibrosis, alleviated epithelial-mesenchymal transition and oxidative stress in hyperuricemia mice. Thus, we concluded that baicalein executed a kidney-protection action in hyperuricemia and therefore may be used as a therapeutic alternative for hyperuricemic nephropathy.