In the present study, a surface-active enzyme, lipase was immobilized in polyethyleneimine (PEI) microcapsules and then modified with oxidized multiwall carbon nanotubes (MWCNTs). The resulting lipase microcapsules exhibited higher activity and stability, since the activity of microcapsules was 21.9 folds than that of the free counterpart. Numerous interfaces which were created in polycondensation enhanced the performance of lipases. Illustrated by confocal laser scanning microscope (CLSM), it was found that microcapsules, whose barrier properties against molecules with diameter >4.6 nm, were with a semipermeable and porous membrane structure. The lipases preferred to locate in the wall of the microcapsules. The oxidized multiwall carbon nanotubes (MWCNTs) were further added to modify microcapsules, resulting in even higher activity. The nanocomposites were examined by scanning electron microscope (SEM) and zeta-potential analyzer. The results indicated the superior catalytic performances were attributed to the augmented interface and decreased positive charge. Finally, the MWCNTs modified microcapsules were utilized in producing biodiesel with a 97.15% yield and retained nearly 90% yield after running 10 cycles. This approach of microcapsulation will be highly beneficial for preparing various bio-active microcapsules with excellent catalytic performance.