Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been enthusiastically adopted in clinical microbial identification by virtue of its rapid process, easy operation, relatively low cost and high throughput. However, its identification accuracy for common clinical pathogens is still inconclusive. Therefore, we conducted this meta-analysis to systematically assess the performance of MALDI-TOF MS in identifying clinical pathogenic bacteria and fungi by meta-analysis. After a comprehensive literature search through PubMed and Web of Science databases (up to January 2016), 50 articles involving 35406 bacteria isolates and 30 articles involving 14250 fungi isolates were included. Overall analysis demonstrated that the accuracy of MALDI-TOF MS for bacteria identification increased from 0.849 (95% confidence interval (CI) = 0.812-0.879) at the species level to 0.909 (95% CI = 0.883-0.933) at the genus level; the accuracy of MALDI-TOF MS for fungi identification increased from 0.922 (95% CI = 0.900-0.941) at the species level to 0.942 (95% CI = 0.926-0.956) at the genus level. Then we performed univariate and multivariate meta-regression analyses to explore potential factors of heterogeneity. Subgroup analyses were also carried out to further evaluate the identification accuracy of MALDI-TOF MS in various clinical situations, which including different strain categories, pre-treatments, specimen types and detection systems. In summary, our meta-analysis not only strongly suggests that MALDI-TOF MS truly is a good diagnostic tool for clinical microbiology, but also provides several hints to improve its performance in the coming future.