Self-organizing nanostructure evolution through spinodal decomposition is a critical phenomenon determining the properties of many materials. Here, we study the influence of stress on the morphology of the nanostructure in binary alloys using atomistic modeling and atom probe tomography. The atomistic modeling is based on the quasi-particle approach, and it is compared to quantitative three-dimensional (3-D) atom mapping results. It is found that the magnitude of the stress and the crystallographic direction of the applied stress directly affect the development of spinodal decomposition and the nanostructure morphology. The modulated nanostructure of the binary bcc alloy system is quantified by a characteristic wavelength, λ. From modeling the tensile stress effect on the A-35 at. pct B system, we find that λ001<λ111<λ101<λ112 and the same trend are observed in the experimental measurements on an Fe-35 at. pct Cr alloy. Furthermore, the effect of applied compressive and shear stress states differs from the effect of the applied tensile stress regarding morphological anisotropy.