Screening of foodborne pathogens is an effective way to prevent microbial food poisoning. A microfluidic biosensor was developed for rapid and sensitive detection of Salmonella Typhimurium using quantum dots (QDs) as fluorescent probes for sensor readout and manganese dioxide nanoflowers (MnO2 NFs) and as QDs nanocarriers for signal amplification. Prior to testing, amino-modified MnO2 nanoflowers (MnO2-NH2 NFs) were conjugated with carboxyl-modified QDs through EDC/NHSS method to form MnO2-QD NFs, and MnO2-QD NFs were functionalized with polyclonal antibodies (pAbs) to form MnO2-QD-pAb NFs. First, the mixture of target Salmonella Typhimurium cells and magnetic nanoparticles (MNPs) modified with monoclonal antibodies (mAbs) was injected with MnO2-QD-pAb NFs into a microfluidic chip to form MNP-bacteria-QD-MnO2 complexes. Then, glutathione (GSH) was injected to dissolve MnO2 on the complexes into Mn2+, resulting in the release of QDs. Finally, fluorescent intensity of the released QDs was measured using the fluorescent detector to determine the amount of Salmonella. A linear relationship between fluorescent intensity and bacterial concentration from 1.0 × 102 to 1.0 × 107 CFU/mL was found with a low detection limit of 43 CFU/mL and mean recovery of 99.7% for Salmonella in spiked chicken meats, indicating the feasibility of this biosensor for practical applications.