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.