Thinopyrum elongatum (Host) D. R. Dewey as one of relatives of wheat, harboring genes resistance to strip rust and Fusarium head blight and tolerance to salinity for wheat improvement, could be used for wheat genetic improvement. To understand the effects of chromosome 1Ee on wheat agronomical and quality-related traits, wheat-Th. elongatum chromosome disomic substitution line 1Ee(1A) from common wheat cultivar Chinese spring was analyzed in multiple environments. In relative to the Chinese Spring, the substitution line showed the reduction of the length and width of wheat flag leaf, the length and width of kernels, no. of spikelets per spike, no. of kernels per spike and thousand kernel weight. However, the length of spikes (P < 0.05) was significantly increased. Regarding to the quality-related traits, the substitution line displayed the increases of the dough max peak height and band width of 8 min, but no differences of the grain protein content, SDS sedimentation, wet gluten content, gluten index and peak height time were observed. In addition, 17 COS markers specific to chromosome 1Ee were developed in this study. All in all, chromosome 1Ee can improve wheat grain quality traits, but it has negative effects on yield related traits. And the developed markers specific for chromosome 1Ee might be used for developing wheat-Thinopyrum chromosome short segment lines carrying Glu-Ee1 by reducing the chromosomal linkage drag.