Objective The microfluidic chip detection platform was used to detect bacterial 16srDNA in platelet concentrates by real-time quantitative PCR with Taqman fluorescent probes, and the application of this system in the rapid detection of bacterial contamination in platelets was discussed. Methods The suspension of Staphylococcus aureus or Pseudomonas aeruginosa were artificially added to the platelets to simulate the blood samples contaminated by bacteria. While platelets without bacteria were set as blank control and sterile water was set as negative control. After 10-fold gradient dilution, the relative experiments such as bacterial counts, bacterial genomic DNA extraction, bacterial 16sDNA detection by microfluidic chip FQ-PCR were carried out. The specificity, sensitivity and repeatability of the microfluidic chip FQ-PCR detection system were evaluated. Results The probes and primers responded to the positive reference, but did not respond to blank control. For Staphylococcus aureus contamination of platelets, the sensitivity of this method was 865CFU/mL and for Pseudomonas aeruginosa, the sensitivity was 885CFU/mL. When the bacterial content of Staphylococcus aureus was 865CFU/mL, the difference of Ct value between the blank control group and bacterial group was 4.35±1.01; and for Pseudomonas aeruginosa (885CFU/mL), the difference was 2.03±0.61. The repeatability index of Ct values of bacterial with various concentrations ranged from 0.012 to 0.052. Conclusion Based on the microfluidic chip detection platform, the TaqMan probe FQ-PCR system can do well to detect bacterial contamination of platelets. It can be applied to the rapid detection of bacterial contamination before platelet transfusion when the sensitivity and repeatability of the system have been improved.