To overcome the poor timeliness and the low automaticity of existing aquaculture 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 aquatic pathogens antibody on its surface. The aquatic pathogens are captured by magnetic beads because of the induction and control of the external Gauss magnetic field. The combination of aquatic pathogens and beads is induced to the microelectrode array. The content of aquatic pathogens can be detected effectually by the counting circuit based on impedance measurement fixed at the electrode terminals. The research results show that the amount of aquatic pathogens can be detected effectively by this system. Moreover, the proposed system can reduce the detection time to onesixtieth compared with traditional laboratory test.