The invention discloses a trace amount microorganism quick detection system which includes a scanning light path unit and a control unit. The scanning light path unit includes a laser device, a beam expanding lens, a first grating, a first light filter set, a second light filter set, a dichroic mirror, a two-dimensional scanning galvanometer, a scanning lens, a lens, a second grating and a photoelectric detector. The scanning light path unit is used for filtering incident laser, focusing light beam, moving a light spot, separating the incident laser and a fluorescent signal, and converting a photoelectric signal. The control unit includes a two-dimensional galvanometer control card, a data collection card and a terminal controller. The data collection card converts an analogue electric signal, which is outputted to the photoelectric detector, into a digital electric signal, and sends data to the terminal controller for processing the data, thereby finally displaying a two-dimensional image. The system is mainly used for detecting and counting fluorescently-dyed microorganisms attached to the surface of a micropore filter membrane and achieves the quick scanning detection on the microorganisms in trace amount.