Candida rugosa lipase (CRL) was immobilized on an aminopropyl-functionalized MSU-H type mesoporous silica (AFMS) through physical adsorption and a covalent cross-linking. It was evaluated as a class of biocatalysts in the esterification of conjugated linoleic acid (CLA) isomers with ethanol. AFMS materials with varied content of aminopropyl were prepared by a simple co-condensation at near neutral pH condition. Introduction of aminopropyl chains and CRL molecules onto the AFMS supports was confirmed by Fourier transform infrared (FT-IR) spectra. CRL was immobilized on the AFMS through electrostatic and covalent interactions. The covalently cross-linked CRL gave a loading amount of 34.3mg CRL/g-support and a hydrolytic activity of 2471.5U/g-catalyst. It exhibited high operational stability and remained 23.9-27.5% of total esterification in 32 h consecutive four runs in the esterification of CLA with ethanol. Moreover, the immobilized CRLs catalyzed 2.8-3.8 times of esterification of cis-(c)9, trans-(t)11-CLA faster than that of t10, c12-CLA.