Wheat is a globally important food crop, which provides 20% of total calories consumed by human beings. To secure food safety, we must increase the wheat yield potential in the coming decade. Improving the stem traits is critical to develop elite varieties. We have previously identified a mutant showing a quick stem elongation rate derived from heavy ion beam mutagenesis. The stem of mutant elongates quicker than wild type, but the mutant shows same mature plant height as wild type plant. To dissect the molecular mechanism underlying the mutant phenotype, we compared the transcriptome data for mutant and wild type. There were totally 4,340 differentially expressed genes (DEGs) were identified between the mutant and wild-type. These DEGs were subsequently employed for GO and KEGG analyses. Benzoxazinoid biosynthesis pathway-associated genes were significantly enriched by KEGG analysis. Genes encoding the benzoxazinoid biosynthesis enzymes Bx1, Bx3, Bx4, Bx5 and Bx8_9 were confirmed by qPCR to be differentially expressed between mutant and wild type. It suggested that benzoxazinoids could play critical roles in regulating the stem elongation phenotype of the mutant. To finely map the underlying mutated gene, namely qd1, in this mutant, we analyzed F2 and BC3F2 segregating populations. The qd1 gene was ultimately mapped to a 1.33 Mb interval from 28.86 Mb to 30.19 Mb on chromosome 4B. Among the four candidate genes in this region, the gene of TraesCS4B02G042300 was considered to be the mutated gene, since that its expression pattern was concurrent with the stem development of the mutant and wild type. This gene can be further used to manipulate stem development in the future.