In this study, a new immobilization method was exploited to encapsulate β-galactosidase (β-gal) from Aspergillus oryzae using aggregated core–shell silica nanoparticles as a matrix. Transmission electron microscopy (TEM) and Fourier transform infrared (FTIR) spectroscopy were used to characterize the material encapsulated β-gal. Compared to the free β-gal, the encapsulated β-gal shows a broader pH tolerance and thermal stability. Furthermore, the encapsulated β-gal shows better storage stability over 30 days. After nine cycles of hydrolytic reaction, the encapsulated β-gal still maintains 94.2% of its initial activity, which indicates that the β-gal exhibits excellent reusability after encapsulation.