The invention provides a single-cell ATAC-seq data analysis method. The single-cell ATAC-seq data analysis method comprises the following steps: S1, performing data analysis and quality control on sequencing original data; S2, performing comparative analysis; S3, analyzing an insertion fragment; S4, carrying out Peak analysis on the enrichment region; S5, classifying the single-cell subgroups; S6,carrying out annotation and enrichment on the Peak related genes; S7, carrying out TF-motif analysis; S8, carrying out the subgroup accessibility difference analysis; S9, analyzing related genes of the difference accessibility sites, and annotating genes corresponding to the transcription start sites closest to the peak region where the identified difference TF-motif is located, and the like. According to the method, a comprehensive single-cell ATAC-seq data analysis process with rich analysis contents is constructed; the analysis result reveals a large amount of biological information, people can deeply excavate biological phenomena and characteristics contained in the single-cell level conveniently, the analysis process and result are visually displayed in the form of html, the analysiscontent is clear in hierarchy, the result display forms are diversified, and the readability of the report is improved.