Microreactors engage the attention of researchers and engineers in the pharmaceutical and chemical industries as well as universities. When the production capacity of micro chemical plants is increased by numbering-up approach, it is important to realize the uniform flow distribution among the parallelized microreactors. In addition, a blocked microreactor needs to be identified as early as possible to achieve the stable long-term operation of micro chemical plants. However, it is not practical to install the sensors in all the microreactors from the viewpoint of cost or space. In this research, a system that can detect and diagnose a blocked microreactor by using just two flow sensors is developed. The effectiveness of the developed system is demonstrated by numerical and experimental investigations, and it is clarified that the developed method has high robustness to changes in the fluid properties and the microreactor characteristics such as pressure drop. The developed system will be applicable to various types of micro chemical plants with parallelized microreactors.