Compared to traditional enzyme immobilization techniques, organic-inorganic hybrid nanoflowers (HNFs) are an effective method for enzyme immobilization that can enhance the stability and catalytic activity of free enzymes. Therefore, in this study, glucose oxidase (GOD) and horseradish peroxidase (HRP) were used as the organic components, phosphate copper was used as the inorganic component, and a bienzyme-inorganic hybrid nanoflowers biocatalyst (referred to as biE-HNFs) was prepared using a co-milling self-assembly growth method. The biE-HNFs exhibited complete flower-shaped morphology, the largest specific surface area, highest enzyme activity, and highest loading enzyme concentration when the bienzyme concentration was 1.0 mg mL–1, incubation time was 72 h, HRP-GOD bienzyme concentration ratio was 2:1, phosphate-buffered saline solution (PBS) concentration was 0.10 M and Cu2+ concentration was 0.12 M. Furthermore, compared to free bienzyme, biE-HNFs demonstrated better temperature stability, pH stability, and storage stability. Even after 60 days of storage, the indole degradation rate remained above 90 %. Using organic-inorganic hybrid nanoflowers for immobilizing bienzyme not only retains the advantages of high activity and large specific surface area, but also allows for synergistic effects between HRP-GOD bienzyme in indole degradation, suggesting a new approach for efficient removal of indole by immobilizing bienzyme.