As one of the important relative species of common wheat, Th. intermedium (2n = 6x = 42, EeEeEbEbStSt or JJJSJSStSt) possesses many valuable traits in wheat improvement. In this study, the evolution relationship, natural selection pressure of Th. intermedium and its five relatives were analyzed by the method of comparative transcriptomics. We estimated the synonymous rate, non-synonymous rate, and evolutionary constraint between pairs of orthologous genes from Th. intermedium (2n=6x=42, EeEeEbEbStSt or JJJSJSStSt) and its relatives Th. elongatum (2n=2x=14, EeEe), Th. bessarabicum (2n=2x=14, EbEb), Pseudoroegneria strigose (2n=2x=14, StSt), Dasypyrum villosum (2n=2x=14, VV), and Th. ponticum (2n=10x=70, EeEeEbEbExExStStStSt or JJJJJJJSJSJSJS). Transcriptome analyses reveal that only a fraction of orthologous genes exhibit un-conserved expression patterns. Totally 44 divergent genes were found, accounts for only 1.0% homologous genes. The functions of these genes are related to molecular function and biological process. The bayesian phylogenetic tree of Th. intermedium and its five relatives shows that Th. ponticum is more closed with Th. elongatum and Th. bessarabicum than Th. intermedium, and Th. intermedium is closed grouped with D. villosum and the Ps. strigosa subclades. These findings illustrate that in addition to Ps. strigosa, Th. elongatum and Th. bessarabicum, the origin genome donor of Th. intermedium probability contains D. villosum. Under natural selection, the evolution of plants tends to conservative rather than divergence.