In this study, two new calixarene derivatives bearing thiourea and carbamate moieties were synthesized and characterized. Moreover, thiourea- and carbamate-bridged calixarene derivatives with Fe3O4 magnetic nanoparticle were employed for the first time as the convenient additives in the encapsulation process of lipase. The results of catalytic activity and enantioselectivity of the encapsulated lipases in the hydrolysis reaction of racemic flurbiprofen methyl ester indicate that both of the encapsulated lipases (Enc-TuC[4]@Fe3O4 and Enc-CbC[4]@Fe3O4) exhibit higher conversion and enantioselectivity compared to the free-encapsulated lipase (Enc-Lipase). However, the highest affinities result was obtained when the encapsulated lipase (Enc-CbC[4]@Fe3O4) was used in the kinetic resolution reaction of racemic flurbiprofen methyl ester.