Background: The availability of rapid, sensitive, and simple diagnostic methods is essential for the control of the highly contagious and rapidly transmitted respiratory viral infections. The colloidal gold strips method, the most widely used antigen detection, provides a simple and rapid assay but suffers from the low sensitivity. The purpose of this study was to develop a rapid and sensitive method for detecting the antigen of influenza A virus. Methods: We developed an Immuno-recombinase -aided amplification (IRAA) assay for ultrasensitive detection of Influenza B virus antigen. IRAA was based on recombinant human mannan-binding lectin (rhMBL, M1 protein)-encapsulated magnetic beads (M1 magnetic beads) to efficiently enrich the Influenza B virus particles from the clinical sample. The detection antibody-ssDNA complex was subsequently bound to the M1 magnetic beads. Finally, ssDNA was amplified using the RAA assay. In parallel, the colloidal gold strip assay for Influenza B virus antigen was compared. Using 64 clinical pharyngeal swab specimens, we explored the specificity, sensitivity and applicability of the newly developed IRAA. Results: The limit of detection of IRAA assay was 0.125pg/mL (BY) and 0.013 pg/mL (BV) of Influenza B virus, which was a 10,000-fold increase in detection sensitivity compared to colloidal gold assays. Moreover, the detection specificity of the IRAA for Influenza B virus was 95.6%. Conclusions: Our results demonstrated that IRAA assay has remarkable potential for the early, rapid and sensitive differential diagnosis of Influenza B virus in the point-of-care testing after more sample validation and optimization.