Wheat grains are an important source of human food but current production amounts cannot meet world needs. Several environmental constraints such as heat could potentially negatively affect wheat production. Therefore, it is important to understand the response of grains during the development to an increase of ambient temperature in a global warming context. Plants from two wheat genotypes have been submitted to two growth temperature regimes. One set has been grown at optimal mean daily temperature of 19°C while the second set of plants has been submitted to warming at 27°C from 2 days after anthesis (daa) to 13 daa. Gene expression was evaluated using micro-array during nine different seed developmental stages and agronomic traits were measured at harvest. While warming did not affect mean grain number per spike, it significantly reduced other yield-related indicators such as grain width, length, volume and maximal number in the endosperm. Whole genome expression analysis identified 6,258 and 5,220 genes whose expression was affected by temperature in the two genotypes respectively. The greater difference between low and high temperature was displayed at a key stage 120°C days after anthesis (°Cd) which suggest that significant transcriptional changes occur during the transition that encompasses the 120°Cd stage in response to warming. Co-expression analysis using WGCNA uncovered modules associated with agronomic traits. In particular, modules enriched in genes related to nutrient reservoir and endopeptidase inhibitor activities were found positively associated with cell number in the endosperm. A hypothetical model pertaining to the effects of warming on gene expression and growth in wheat grain is proposed. Network analyses suggest a negative effect of the expression of genes related to seed storage proteins and starch biosynthesis upon moderately high temperature on the grain size in wheat.