Nitrile hydratase cross-linked enzyme aggregates (CLEAs) were formed in mesoporous onion-like silica (NHase-CLEAs@MOS) by using macromolecular dextran polyaldehyde as a cross-linker through the carrier-bound CLEAs method. The effect of preparation parameters on the recovery of enzyme activity was investigated. The properties such as pH, thermal and storage stability, and kinetic parameters of NHase-CLEAs@MOS were also studied. The maximum amount of NHase absorbed in MOS was 535 mg/g. Under optimized conditions, the maximum activity recovery of NHase-CLEAs@MOS was 48.2%. The stabilities of NHase-CLEAs@MOS were improved significantly compared to the NHase@MOS prepared by physical adsorption and free NHase. This work demonstrated that the mesoporous onion-like silica can be efficiently employed as host materials for NHase immobilization, and the carrier-bound CLEAs method can lead to enhanced activity and stability of the immobilized enzymes.