Magnetic silica composite particles were prepared by using the biosilicification reaction, in which Fe3O4 nanoparticles were entrapped in a silica matrix. The composite particles were functionalized with 3-aminopropyltriethoxysilane (APTES). These functionalized magnetic composite particles were used to immobilize a kind of valuable bulky industrial enzyme (laccase). The incorporation of magnetic nanoparticles greatly facilitates the manipulation of the immobilized biocatalyst, since it can be easily and quickly recovered from the reaction system by the simple application of an external magnetic field. The effects of immobilization conditions were optimized and the activity of the immobilized laccase was investigated. The results showed that the highest specific activity of immobilized laccase reached to 224 U and the activity recovery was 83.9%. Compared with free laccase, the thermal, pH, operational and storage stabilities of the immobilized laccase were improved significantly. The catalytic activity of the immobilized laccase was also demonstrated by the degradation of two phenolic substances (i.e., 2,4-dichlorophenol and 4-chlorophenol). It was found that the removal rates of 2,4-dichlorophenol and 4-chlorophenol were 80.9% and 64.2% in about 12 h, respectively.