Objective To evaluate the accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying common clinical fungi, and provide evidence for the diagnosis and treatment of fungal infection. Methods Literatures about the accuracy of MALDI-TOF MS in fungal detection were searched through databases by computer, after quality evaluation and data extraction of the included literatures were performed, bias risk of included literatures was evaluated by QUADAS-2 tool, Meta-Disc 1.4 software was used for Meta-analysis, diagnostic efficacy of different sources of strains, species of strains, reference methods and instrument use in each subgroup were compared. Results A total of 26 articles and 9 708 strains of fungi were included, covering the common clinical yeasts and filamentous fungi. Meta-analysis showed that the combined sensitivity (95% CI), combined specificity (95% CI), combined positive likelihood ratio (95% CI), and combined negative likelihood ratio (95%CI) were 0.97 (0.97-0.97), 0.85 (0.81-0.88), 5.60 (4.55-6.90), 0.02 (0.01-0.04), and 282.40 (149.50-533.46) respectively, the area under summary receiver operating characteristic (SROC) curve was 0.9078. The results of subgroup analysis showed that MALDI-TOF MS technique has a good effect on identifying clinical yeasts and filamentous fungi, which is not affected by the source of strains, instrument brand and other factors. Conclusion MALDI-TOF MS is highly accurate for the identification of clinical pathogenic fungi, it is suitable for wide clinical application.