In this study, we developed a QDs-based lateral flow immunoassay system (QD-LFIAS) to simultaneously detect influenza A virus subtypes H5 and H9. We synthesized water-soluble carboxyl-functionalized QDs and covalently bound them to influenza A virus antibodies. We selected subtypes H5 and H9 as the target pathogen and evaluated the detection time and sensitivity; we also measured the detection specificity and reproducibility of the QD-LFIAS.