A multicomponent reaction is established toward quinazolimine derivatives, but it requires intensive human interventions in conventional reaction systems to suppress the side reactions. Herein, an automated microfluidics‐based reaction system that uses a program to command the fluid conductance to perform a cascade of reactions and separation in a defined sequence is innovated. The system is composed of chained reaction modules. Within the individual reaction module, side reactions are suppressed by creating an extremely high concentration bias between the reagents via selective reagent diffusion through the porous channel wall. The reaction sequence is commanded by transporting reagents from one module to the following ones, obtaining quinazolimine derivatives with high yield and purity. The system is low cost, easy to compose, program commanded, and requires minimal human intervention once the reaction modules are assembled and reagents are loaded.