The development of molecular biology can not be separated from the development of sequencing technology.High-throughput sequencing technology is known as the second-generation sequencing technology.Compared with the sanger sequencing technology,it is high-throughput,fast,and low costs.This article describes the application of the high-throughput sequencing technology from three levels,including genome level of resequencing,de novo sequencing and metagenomic sequencing,RNA level of transcriptome sequencing and small RNA sequencing,and epigenetic level of DNA methylation and transcription factor binding sites.