With the aim to provide a highly stable and active biocatalyst, cross-linked enzyme aggregates (CLEAs) of lipase Candida sp. 99-125 were prepared in three-dimensionally ordered macroporous silica materials (CLEAs-LP@3DOM-SiO2). Lipase Candida sp. 99-125 was first precipitated in the pores of 3DOM SiO2 (named EAs-LP@3DOM-SiO2), and further cross-linked by glutaraldehyde to form CLEAs-LP@3DOM-SiO2. Saturated ammonium sulfate was used as a precipitant and glutaraldehyde with a concentration of 0.25% (w/w) was employed as a cross-linker. Compared with EAs-LP@3DOM-SiO2 and native lipase, CLEAs-LP@3DOM-SiO2 exhibited excellent thermal and mechanical stability, and could maintain more than 85% of initial activity after 16 days of shaking in organic and aqueous phase. When CLEAs-LP@3DOM-SiO2 was applied in esterification and transesterification reactions, improved activity and reusability were achieved. This method can be used for the immobilization of other enzymes of interest.