Post-flowering shading may change the accumulation and structure formation of starch in wheat, resulting in deterioration of flour processing and edible qualities. But the effects of post-flowering shading on physicochemical properties and the intrinsic relationship between the starch components and physicochemical properties in wheat starch was still unclear. We observed that the changes of starch components and physicochemical properties under different shading intensity (the photosynthetic active radiation was cut off by 0%, 30%, and 60%) after flowering in waxy wheat cultivar Nongdanuo 50222 and non-waxy wheat cultivar Lunxuan 987. In this study, we found the starch content decreased, however, the proportion of A-type starch granules and the relative crystallinity increased in both cultivars under shading stress. Meanwhile, the starch peak viscosity, hold trough, final viscosity, breakdown, and setback in Lunxuan 987 showed increasing trends with the increase of shading intensity. On the contrary, those in Nongdanuo 50206 showed decreasing changes. In Lunxuan 987, stronger shading stress led to decreased onset temperature, peak temperature, and end temperature, but increased gelatinization enthalpy. In Nongdanuo 50206, these starch thermodynamic parameters all decreased with the increase of shading intensity. The correlation analysis showed that amylose content, amylose/amylopectin ratio, and A-type starch granules volume proportion were positively correlated with the relative crystallinity, peak viscosity, hold trough, breakdown, pasting temperature, and gelatinization enthalpy, but negatively correlated with final viscosity and setback. Our findings suggested that post-flowering shading stress has the negative effects on starch components and particle size distribution, thus, resulting in the changes of relative crystallinity, gelatinization, and thermodynamic properties of wheat starch.