The English grain aphid, Sitobion avenae Fabricius (Hemiptera: Aphididae), and bird cherry-oat aphid, Rhopalosiphum padi L. (Hemiptera: Aphididae), are two common herbivore pests that have devastating effects on wheat production worldwide. To tolerate herbivores, plants coevolved various biological and morphological features. The present study focused on the characterization of the S. avenae- and R. padi-tolerant features in the winter wheat line XN98-10-35 under field conditions. The yield loss experiment revealed that XN98-10-35 presented strong tolerance to S. avenae and R. padi feeding, as we observed a small 100-kernel weight decrease induced by S. avenae and R. padi. Examination of the ultrastructure of the flag leaves revealed that XN98-10-35 exhibited a greater number of stomata and a larger stomata size than the controls. In comparative gene expression profiling tests, the expression levels of the candidate genes SaEST1 and SaEST2, which are putative photosystem I assembly protein Ycf3 and vegetative cell wall gp1-like protein, were up-regulated several-fold in the flag leaves of XN98-10-35. Additionally, genes associated with sucrose synthase and starch synthase were up-regulated in the flag leaves of XN98-10-35. These findings increase our understanding of the molecular mechanism underlying tolerance to S. avenae and R. padi infestations in XN98-10-35 and will allow rapid breeding of tolerant cultivars.