A microchemical system, constructed with two micromixers and a delay loop, is designed to carry out the organocatalyzed Beckmann rearrangement of cyclohexanone oxime to ε-caprolactam with trifluoroacetic acid as the catalyst. In the microsystem, cyclohexanone oxime which is dissolved in acetonitrile mixes with trifluoroacetic acid in the first micromixer to realize uniform reaction condition, and then the mixture passes through the delay loop to continue the reaction. Finally, a large amount of acetonitrile is pumped into the second micromixer to stop the reaction by cooling and diluting the reaction system. The viscosity and reaction enthalpy of the organic reaction system are determined. The results show that both two are favorable for avoiding the clogging, increasing the heat transfer and improving the process safety. Two different catalytic systems are adopted and elevated in this microsystem. The influences of temperature, residence time, and oxime concentration on the reaction performance are investigated. Under optimized conditions, the reaction can be accomplished with a residence time less than 48 s and the selectivity of 99+%. The results show that Beckmann rearrangement can be realized in the microsystem with much more efficiency and safety.