Objective To assess the performance of three metagenomic-next generation sequencing (mNGS) platforms. Methods 18 reference and 8 clinical specimens were performed mNGS by three platforms (A, B and C). Sensitivity, specificity, negative predictive value and positive predictive value were analyzed. Results For reference, sensitivity of platform A, B and C were 97.8%, 100%, and 45.1%; specificity were 50.0%, 100% and 100%; negative predictive value were 25.0%, 100% and 3.8%; positive predictive value were 87.3%, 75.2% and 93.2%. As for clinical specimens, sensitivity of platform A, B and C were 87.0%, 82.6% and 87.0%; positive predictive value were 90.9%, 65.5% and 60.6%. Conclusion This research enriches the data in domestic mNGS platform, and provides suggestions for the development of new diagnostic technologies for infectious diseases.