In allusion to the poor timeliness and the low automaticity of existing pathogen detection, an integrated microfluidic system for rapid detection is proposed. The microelectrode is set on the bottom of the microfluidic channel and connected to a digital impedance measurement circuit in this system. The magnetic beads is encased by the pathogens antibody on its surface. The pathogens are captured by magnetic beads because of the induction and control of the external Gauss magnetic field. Then the combination of pathogens and beads is induced to the microelectrode array. The content of pathogens can be detected effectually by the counting circuit based on impedance measurement which is established at the electrode terminals. It is shown by the results of the research that the amount of pathogens can be detected effectively by this system as this system can reduce the time of the detection to one-sixtieth compared with traditional laboratory test.