Lipase-inorganic hybrid nanoflowers were prepared using Ca3(PO4)2 as the inorganic component and lipase from Aspergillus oryzae (A. oryzae) as the organic component. The influences of metal ions with different valence, various additives (surfactant), and synthesis conditions on the activity of the lipase hybrid nanoflowers were systematically investigated. Results revealed that the valence state of metal ions played an important role on the shape and activity of lipase hybrid nanoflowers. The synthesized lipase hybrid nanoflowers using bivalence metal ions (Ca2+, Mn2+, and Zn2+) as the inorganic components exhibited relative high activity. However, very low activities were observed in the lipase hybrid nanoflowers using univalent metal ions (Ag+) or trivalent metal ions (Al3+, Fe3+). More importantly, Ca2+ not only induced self-assemble of lipase hybrid nanoflowers, but also activated the enzyme activity by inducing conformational changes in lipase from A. oryzae. As a result, lipase/Ca3(PO4)2 hybrid nanoflowers (hNF-lipase) exhibited the high activity. The hNF-lipase displayed 9, 12, and 61 folds higher activity than lipase/Ag3PO4 hybrid nanoflowers, lipase/AlPO4 hybrid nanoflowers, and lipase/FePO4 nanoflowers, respectively. Compared with free lipase, the hNF-lipase displayed 172 % increase in activities by using 0.15 mM Tween-80 as an activity inducer (activated hNF-lipase). Furthermore, the hNF-lipase and activated hNF-lipase exhibited increased stability against high temperature and denaturant, and had good storage stability and reusability.