Wild wheat is a heterologous hexaploid with a large genome size (about 14 GB) and a lot of repetitive sequences. In order to breed new varieties with good traits, we must first locate the genes that control the target traits. Therefore, it is important to establish a complete and accurate genome annotation process. Traditional genomic annotation method based on database alignment has three obvious disadvantages:first, the alignment runs slowly; second, it is difficult to discover new genes; third, there is no uniform standard for software selection. We propose a new analysis process that combines genetic database alignment, transcriptome high-throughput sequencing, and full-length transcriptome single-molecule sequencing data analysis to annotate hexaploid wheat KN9204 completely and accurately. The annotation of the genome provides an important reference and technical support for revealing the growth of wheat and cultivating new varieties.