The present invention provides a single-cell ATAC-seq data analysis method, comprising the following steps: Step S1, performing data analysis and quality control on the sequencing raw data; Step S2, comparing analysis; Step S3, inserting fragment analysis; Step S4, enriching Peak analysis of set area; step S5, classification of single-cell subgroups; step S6, annotation and enrichment of Peak-related genes; step S7, TF-motif analysis; step S8, difference analysis of subgroup accessibility; step S9, difference Accessibility site-related gene analysis, gene annotation corresponding to the transcription start site closest to the peak region where the identified differential TF-motif is located, etc. The present invention constructs a single-cell ATAC-seq data analysis process that is comprehensive and rich in analysis content. The analysis results reveal a large amount of biological information, which is convenient for people to dig deep into the biological phenomena and characteristics hidden in the single-cell level, and analyze the process and results. Visual display in the form of html, the level of analysis content is clear, and the results are displayed in various forms, which increases the readability of the report.