Microreactors with parallel microchannels are widely used in the chemical industry to expand the production rate of micro reactors. Although this provides compact reactor architecture at reasonably high throughput, a sophisticated monitoring system is necessary to diagnose blockages in the microreactor to ensure stable and efficient operation. We propose a method to estimate the blockage degree of microchannels when blockages occur in two microchannels simultaneously. The method involves comparing measured pressure data, and pressure data calculated using the pressure drop model at the sensor locations closest to the identified blocked microchannels. We applied this method to estimate the degree of blockage of a microreactor with ten microchannels. The results of CFD simulations showed that the method made it possible to accurately estimate the blockage degree using fewer pressure sensors than there are microchannels.