The invention provides an automatic analysis method for bacterial whole genome sequencing data, which comprises the following steps: acquiring bacterial genome sequencing data, and judging the type of the sequencing data; respectively carrying out corresponding preprocessing according to the type of the sequencing data; performing re-sequencing analysis and de novo sequencing analysis on the preprocessed sequencing data according to an analysis type selected by a user and preset tool software and software parameters; and realizing the identification and annotation of the whole genome of the bacteria. The scheme provides a user-friendly automated analysis method, for researchers and clinicians without professional bioinformatics knowledge, automated bioinformatics analysis steps including sequencing quality control, re-sequencing and de novo assembly, similar bacterial reference genome identification, bacterial genome annotation, and at the same time, researchers and clinicians without professional bioinformatics knowledge; meanwhile, customized bioinformatics analysis can be carried out according to short-read-length and long-read-length sequencing data generated by different platforms, and an accurate analysis result is obtained.