Fusarium head blight (FHB) caused by Fusarium graminearum species complex is a destructive disease in wheat worldwide. Lack of FHB resistant germplasm is a barrier in wheat. Thinopyrum elongatum is an important relative species successfully used for genetic improvement in wheat. In this study, the translocation lines with different size of chromosome fragment of diploid Th. elongatum 7EL were created by 60Co-γ radiation. FHB resistance gene of diploid Th. elongatum was located on the 7EL physical map constructed by molecular markers of chromosome fragment breakage sites. A stable inheritance translocation line SF7EL9 with hard resistance to FHB was obtained and used as a doner to transfer FHB resistant gene to commercial varieties in wheat. SF7EL9 was further used to explore the genes related to FHB resistance, the gene expression was analyzed in different times after Fusarium graminearium inoculation by transcriptome sequencing, nine genes including GST gene, calcium-binding protein gene, cytochrome P450 gene were significantly up-regulated after pathogen inoculation. Sequence alignment showed that there were 10 amino acid loci differences in the GST protein between diploid and decaploid of Th. elongatum. Therefore, whether diploid and decaploid of have the same genes to FHB resistant needs to be further studied.