In this study, phenylalanine ammonia lyase (PAL) is used as model, and the cross-linked enzyme aggregates of PAL with crude-pored microspherical silica core (NH-PAL-CLEAs) are prepared. The conditions for the preparation of NH-PAL-CLEAs are optimized. Moreover, some characteristics of the NH-PAL-CLEAs are examined. The optimized conditions for preparing NH-PAL-CLEAs are as follows: 117.75 mg silica, 0.2% (v/v) glutaraldehyde and 1 mL free PAL solution (2 U). Under optimized conditions, the maximum activity recovery of NH-PAL-CLEAs reaches 25%. Compared with PAL-CLEAs, the resulting NH-PAL-CLEAs can be easily separated from the reaction mixture by natural precipitation without centrifugation and filtration treatments. Moreover, NH-PAL-CLEAs show superior operational stability. This technique not only overcomes the difficulty to recover CLEAs due to their small particle sizes and soft for many industrial applications, but also reduces production cycle and energy consumption. As a result, this technique shows superior application prospect for enzyme immobilization.