Lipase PS was immobilized in mesoporous silica (MPS) thin films inside a borosilicate tube microreactor for use in the enantioselective transesterification of vinyl acetate with (±)-1-phenylethanol. The immobilization was tested for 3D cubic and 2D hexagonal MPS thin films inside microreactors with and without hydrophobic treatment. The hydrophobic treatment enhanced the adsorption amount and the lipase activity for both 3D cubic and 2D hexagonal films. Of these treated films, the 3D cubic structure film exhibited the highest yield (64%) with an enantioselectivity higher than 99% in a continuous flow experiment. The activity of the immobilized lipase PS was well maintained for 36-hour continuous operation. A Ping-Pong Bi Bi kinetic model was employed to interpret the activity of the immobilized lipase PS. The ratios of the maximum velocity to the Ping-Pong constant (i.e., specificity constants) were measured for lipase PS immobilized inside the microreactor and for native lipase PS. The value inside the microreactor was 800 times greater than that of the native lipase PS.