The invention discloses a Cronobacter sakazakii CRISPR typing method. The method is as follows: performing DNA sequencing on CRISPR1, CRISPR2, CRISPR3 and CRISPR6 locus sequences of Cronobacter sakazakii, extracting spacer sequences of the four locus sequences, and determining CRISPR type of the Cronobacter sakazakii based on the combination of the four spacer sequences. The method is simple, rapid and low-cost, the resolution of the method is higher than the resolution of MLST typing method, and the Cronobacter sakazakii CRISPR typing method has no environmental pollution, and has low requirements on laboratory equipment and software, CRISPR molecules preserve a lot of information such as historically infected phage and plasmid, by joint with a database, national and even global standardization molecule traceability can be realized, and the method can be extended to the fields of food, inspection and quarantine.