The paper presents a new immunomagnetic-bead-based microfluidic system integrated with an optical detection module for rapid diagnosis of influenza infection. By using the immunomagnetic beads conjugated with influenza-specific antibodies, the developed system can detect influenza viral particles with a high sensitivity and specificity while compared with large-scale systems. The viral particles were firstly recognized and adhered onto the surface of the magnetic beads, then incubated with the developing antibodies labeled with fluorescent dye, and finally detected optically. The developed micro system can perform automatic mixing, transportation and detection of influenza virus within a short period of time and could lead to a crucial platform for biological and medical applications.