The present application provides a method for genotyping M. tuberculosis, comprising obtaining amplifying and obtaining a first DNA fragment from a DNA sample by using one or more primer sets selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50); amplifying and obtaining a second DNA fragment from the obtained first DNA fragment by using one or more extension primers selected from the group consisting of SEQ ID Nos. 51 to 75; and detecting the second DNA fragment by using mass spectrometry, particularly by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).