Magnetic mesoporous silica (MMS) composites with an average mesopore size (~2.98 nm), large surface area (404–442 m2/g), and high saturated magnetization (17.7–33.5 emu/g) were successfully prepared by hydrothermal crystallization in the presence of monodisperse Fe3O4 microspheres. The as‐synthesized composites served as supports for lipase from Burkholderia cepacia (BCL) immobilization in isooctane via interfacial activation and were then employed as biocatalysts for the transesterification resolution of racemic aromatic secondary alcohols to synthesize chiral intermediates. The catalytic performance of the immobilized BCL (BCL/MMS) was notably improved compared to that of the non‐immobilized BCL, with the total conversion and enantiomeric excess reaching 50 and 99% of the maximum theoretical values, respectively. Furthermore, the magnetic BCL/MMS possessing the same textural properties and enzyme loading exhibited decreasing catalytic capability as their saturated magnetization value increased. Moreover, BCL/MMS could also be readily recycled from the reaction system by applying an external magnetic field so as to facilitate its reuse up to five cycles with retaining up to 90% of the initial activity. Its high activity, easy recovery, and excellent operational stability make the BCL/MMS a potential green catalyst for the synthesis of optically active intermediates.