The timeliness and accuracy of test results are crucial factors for clinicians to decide and promptly administer effective and targeted antimicrobial therapy, especially in life-threatening infections or when vital organs and functions, such as sight, are at risk. Further research is needed to refine and optimize matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based assays to obtain accurate and reliable results in the shortest time possible. MALDI-TOF MS-based bacterial identification focuses primarily on techniques for isolating and purifying pathogens from clinical samples, the expansion of spectral libraries, and the upgrading of software. As technology advances, many MALDI-based microbial identification databases and systems have been licensed and put into clinical use. Nevertheless, it is still necessary to develop MALDI-TOF MS-based antimicrobial-resistance analysis for comprehensive clinical microbiology characterization. The important applications of MALDI-TOF MS in clinical research include specific application categories, common analytes, main methods, limitations, and solutions. In order to utilize clinical microbiology laboratories, it is essential to secure expertise through education and training of clinical laboratory scientists, and database construction and experience must be maximized. In the future, MALDI-TOF mass spectrometry is expected to be applied in various fields through the use of more powerful databases.