Silkworm pupae-derived structured lipids are expected to promote the absorption of unsaturated fatty acids, however, low efficiency of bioprocess and low reusability of biocatalyst limit the corresponding biocatalysis technology. Thus, a novel strategy combining magnetic response immobilized lipase and continuous-flow microchannel reactor was proposed to modify silkworm pupae oil. The lipase from Aspergillus niger was immobilized on the surface of chitosan cross-linked magnetic nanoparticles, with increased esterification activity from 151.51 to 418.10 U/g due to the hydrophobic microenvironment. In the microchannel, the enzyme activity could be increased to 2371.3 U/g because of the strengthening effect of the microfluidic field. Furthermore, the employment of chitosan cross-linked magnetic nanoparticles leads to good reusability, and the remaining activity could stay above 90% after 13 cycles. Moreover, the immobilized lipase could be removed and loaded easily due to the employment of magnetically responsive nanoparticles. In addition, 2 min was required to rearrange the unsaturated fatty acids, increasing the relative content of sn-1.3 unsaturated fatty acids from 59.91% to 74.8% and sn-2 palmitic acid from 2.69% to 18.88%, which indicated the improved nutritional value of modified silkworm pupae oil. Therefore, the combination of microfluidic field and hydrophobic microenvironment formed by the chitosan layer on the surface of the nanoparticles effectively strengthens the biocatalysis in a solvent-free system, while the developed strategy provides a convenient biocatalysis strategy for the quality improvement of edible insect oil.