κ-Carrageenan oligosaccharides from κ-carrageenan hydrolysis are important biochemicals with more bioactivity. Enzyme engineering plays a key role in improving κ-carrageenase catalytic efficiency for production of κ-carrageenan oligosaccharides. Effect of metal ions on enzyme activity, especially stability and efficiency, is main factor in catalytic process, but metal ions addition leads to gelation of κ-carrageenan solution. In this study, molecular dynamics simulation was used to explore the interaction between κ-carrageenase CgkPZ and Ca2+, and Ca2+ bonded to D164 and E167 in the catalytic center resulting in the catalytic efficiency increase. Circular dichroism analysis indicated that the secondary structure of κ-carrageenase could change in the presence of Ca2+. Therefore, a novel self-assembly κ-carrageenase-inorganic hybrid nanoflowers CaNF@CgkPZ was synthesized and systematically characterized. The catalytic efficiency (kcat/Km) of CaNF@CgkPZ was 382.1 mL·mg-1·s-1, increased by 292% compared with free κ-carrageenase. Notably, the enzyme activity of CaNF@CgkPZ was not reduced significantly after 19 cycles use, and 70-100% relative activity was still retained when stored at 4-25 ℃ for 15 days. This work provides an efficient approach for κ-carrageenase immobilization with good storage stability, reusability and enhanced catalytic efficiency, which is of great significance in practical applications.