In order to increase application of cross-linked enzyme aggregates (CLEAs) in industry production, a novel micro-reactor system that included a rotating magnetic field (RMF), a micro-reactor and CLEAs with magnetic nanoparticles (M-CLEAs) was designed to synthesize butyl oleate. Result showed that the presence of RMF significantly increased the yield of butyl oleate and the maximum increment was 23%. The yield of butyl oleate was impacted by the dosage and distribution of M-CLEAs in micro-reactor. M-CLEAs showed good reusability, since the morphology and the second structure of protein of M-CLEAs did not show evident change after 4 operative cycles. Although the three-dimensional fluorescence of M-CLEAs showed shift in fluorescence intensity and the maximum emission wavelengths, the yield of butyl oleate was not affected. This study provides a novel design that realized efficient, convenient and continuous application of CLEAs in biosynthesis, and M-CLEAs also show good promises in industry production.