For the higher time consumption, complex constructs and lower detecting accuracy of microbia detection, this research presents a fast, simple microbial detection system with a low detection limit. Combining fluorescence marker, filter membrane, laser scanning and fluorescence imaging technologies, a rapid scanning system for the trace microbia detection was designed. On the basis of the scanning lens with a large field of view, a large depth of field, and a longer focal length, the fast detection for a microbial sample was implemented by combined with a 2D scanning galvanometer. Basic principles of the detection system were described and the optical system was designed and optimized. The collected signals were analyzed, and the performance of the detection system was demonstrated and tested. Experimental results show the detection system accurately detects microbial samples ranged from 10 cfu/mL to 2.5×103 cfu/mL in 10 min, and the detection limit is 10 cfu/mL. The system meets the demands of real-time detection of medical high-purity water and other sensitive detection situations.