The invention relates to the technical field of chemical and pharmaceutical engineering and in particular to a multifunctional continuous flow reaction system. The multifunctional continuous flow reaction system comprises multistage feeding devices, multistage mixing devices, multistage preheating devices, multistage reaction devices, a quenching device, a CIP cleaning device and a blowing and drying device. Reaction tubes in the reaction devices successively communicate through communicating devices, and the feeding devices, the mixing devices, the preheating devices, the reaction devices, the quenching device, the CIP cleaning device and the blowing and drying device are controlled by means of software and a universal hardware platform according to concentration proportion of raw materials needed by chemical reactions and corresponding reaction conditions. The multifunctional continuous flow reaction system provided by the invention is good in mixing effect, precise to control the reaction conditions, uniform in heat transfer and mixing, relatively small in size and occupied space and low in production cost, can continuously realize multistage chemical reactions, and can efficiently master reactant residues in the reaction system and keep the reaction system clean inside.