A processing system and processing method for blocked microreactor. The processing system comprises an gas intake device, a flushing device, a microreactor to be processed and a plasma processing device. One end of the microreactor to be processed is connected with the gas intake device and the flushing device through a pipeline; the other end of the microreactor to be processed is connected with a waste liquid bottle through the pipeline; and the microreactor to be processed is arranged between electrodes of the plasma processing device. The present invention uses the effective reactivity of plasma and active free radicals in an excitation atmosphere to crack micro blockage in a micro channel in a short time. The method of the present invention has high flexibility and strong controllability, and can select plasma electrodes according to blocked regions to crack the blockage in a specific region.