Objective To compare the species identification method of Cronobacter spp. in food, in order to establish rapid, high throughout identification method. Methods A total of 19 Cronobacter spp. in foods were identified with three method including biochemical method using VITEK 2.0 Compact, matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole-genome sequencing (WGS). The advantages and disadvantages of the three identification method were analyzed. Results The result indicated that the accuracy of VITEK identification for C. sakazakii and C. malonaticus was 67% and 66% respectively. However, WGS and MALDI-TOF MS obtained the same result for 19 Cronobacter spp.. Three subspecies could not be identified by MALDI-TOF MS due to the limited database. Conclusion Biochemical method could not be used for species identification of Cronobacter spp. MALDI-TOF MS was rapid, high throughout and accurate, but still need to expand the fingerprint database for more Cronobacter spp. isolates.