In this report, an inflation bulb-driven microfluidic reactor was developed for IR-accelerated proteolysis. This novel proteolysis system mainly consisted of an inflation bulb-driving system, a simple cross-PMMA microchip, and a temperature-controllable IR radiation system. The gas pressure generated from an inflation bulb was employed to drive protein and trypsin solutions to flow into the main channel of the microchip via two capillaries and the injection channel. When the two solutions were mixed in the channel, the protein was rapidly digested by trypsin under IR radiations. The peptides in the digests accumulated in the product reservoir of the microchip were subsequently identified by MS. The feasibility and performance of this unique system were demonstrated by digesting hemoglobin and lysozyme. The results indicated that IR radiation could significantly enhance the on-chip proteolysis and the digestion time was substantially reduced to 5 min. The present proteolysis setup is simple and efficient and will find wide applications in high-throughput protein digestion.