Abstract: Provided is a method for quickly identifying clean transgenic or gene-edited plants and insertion sites by using whole genome re-sequencing data, comprising: extracting genomic DNA; obtaining paired-end sequencing data of a plant whole genome; determining whether an expression vector sequence containing T-DNA sequence, inserted into a plant is known; determining whether transgenic events or gene editing events exist in a plant to be tested, and whether a backbone sequence transfer event occurs; determining the insertion site of the T-DNA sequence. The method combines means of bioinformatic analysis to identify whether there is a transgenic or gene editing event when the expression vector is known or unknown; when the expression vector is known, it not only quickly and accurately provides accurate positioning, direction, copy number and flanking sequence information of the target sequence inserted into genome, but also allows to determine whether there is a backbone sequence inserted into the genome.