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Organic−inorganic hybrid nanoflowers (hNFs), as a novel enzyme immobilization mode, have gained extensive attention in recent years owing to their unique high specific surface area and distinctive microstructure. For the first time, a nuclease P1(NP1)-inorganic hNF (NP1-hNF) was prepared by the self-assembly co-precipitation method using CaCl 2 as the inorganic component and BSA as an inert protein. The hNF microstructure of the prepared NP1-hNFs was confirmed by scanning electron microscopy. With adding inert protein BSA, the NP1-hNFs displayed dramatically enhanced catalytic activity and improved thermal stability compared with the free enzyme. The enzyme activity yield in the immobilization process reached 266%. Comparing with the free NP1, the optimum reaction temperature of the NP1-hNFs increased 10 °C. The NP1-hNFs were further entrapped in calcium alginate microbeads to improve their reusability. The NP1-hNF microbeads retained 65% of residual activity after five recycle uses. Additionally, the microbeads retained up to 96% residual activity after 50 days of storage. This provides a promising route for enzyme immobilization in industrial application.