The design and construction of polymeric compartmentalized structures in water have been intensively explored for controllable catalysis, but the challenge still remains to set up catalytic compartments in organic media. Herein, we designed a simple block copolymer, PCL-b-PEG-b-PCL, to construct a stable and multi-compartmentalized emulsion in an organic solvent by handshaking. This gentle emulsion preparation allowed a successful encapsulation of vulnerable biocatalysts such as benzaldehyde lyase (BAL) and alcohol dehydrogenase (ADH). The compartmentalization provided the emulsion with exceptionally large interfacial area that could enhance BAL activity up to 225 times as compared to the traditional biphasic system. Moreover, the system could be easily scaled up due to its facile preparation with low cost. Therefore, our results pave a way for developing compartmentalized structures in solvents, for biocatalysis in large-scale synthetic chemistry.