Determining the mechanism that effects embolism repair in the xylem vessels of plants is of great significance in predicting plant distribution and the screening of drought-resistant plants. However, the mechanism of perforation plates of xylem vessels in the acceleration of embolism repair is still not clear by using conventional methods of anatomy and visualization technology. Microfluidic devices have shown their ability to simulate physiological environments and conduct quantitative experiments. This work proposes a biomimetic microfluidic device to study the mechanism of perforation plates of xylem vessels in the acceleration of embolism repair. The results proffered that the perforation plates increase the rate of embolism removal by increasing the pressure differential through the vessel, and the rate of embolism removal is related to the structural parameters of the perforation plate. A combination of the perforation size, the vessel diameter and the perforation plate angle can be optimised to generate higher pressure differentials, which can accelerate the process of embolism repair. This work provides a new method for studying the mechanism of microstructures of natural plants. Furthermore, the mechanism that perforation plates accelerate embolism repair was applied to an electrochemical flow sensor for online determination of heavy metal ions. Test results of this application indicate that the mechanism can be applied in the engineering field to solve the problems of reduced sensitivity of devices, inaccuracy of analysis results and poor reaction performance caused by bubbles that are generated or introduced easily in microdevices, which paves the way for applying the theory to engineering.