The opal-like SiO2 microcarriers with different pore diameters named opal-SiO2I and opal-SiO2II were synthesized and utilized as microcarriers to immobilize Rhizopus oryzae lipase (ROL) and Aspergillus oryzae α-amylases (AOA). ROL and AOA can be more stably immobilized on the cross-linked SiO2 opals by neopentyl glycol diglycidyl ether (NGDE), which is the first attempt to use it as a cross-linking agent compared with glutaraldehyde. According to the morphology analysis, multiple layers of SiO2 monodisperse microspheres were regularly packed and formed an opal-like structure, and enzymes were well scattered and immobilized throughout the SiO2 opals. The results showed that the performance of enzymes immobilized on opal-SiO2II with a larger specific surface area was much better than that of opal-SiO2I. The enzyme activity of ROL@opal-SiO2II and AOA@opal-SiO2II cross-linked with 1% NGDE increased 5.32 and 9.32 times compared with their free counterpart, respectively. Furthermore, pH and thermal stability and reusability of ROL/AOA@opal-SiO2II were significantly improved and higher than those of ROL/AOA@opal-SiO2I and free enzymes. This study provides an easily obtained microcarrier opal-SiO2II, which shows potential for efficient different enzyme immobilizations and further industrial applications.