This paper presents a numerical investigation on the behavior of three dimensional granular materials during continuous rotation of principal stress axes using the discrete element method. A dense specimen has been prepared as a representative element using the deposition method and subjected to stress rotation at different deviatoric stress levels. Significant plastic deformation has been observed despite that the principal stresses are kept constant. This contradicts the classical plasticity theory, but is in agreement with previous laboratory observations on sand and glass beads. Typical deformation characteristics, including volume contraction, deformation non-coaxiality, have been successfully reproduced. After a larger number of rotational cycles, the sample approaches the ultimate state with constant void ratio and follows a periodic strain path. The internal structure anisotropy has been quantified in terms of the contact-based fabric tensor. Rotation of principal stress axes densifies the packing, and leads to the increase in coordination numbers. A cyclic rotation in material anisotropy has been observed. The larger the stress ratio, the structure becomes more anisotropic. A larger fabric trajectory suggests more significant structure re-organization when rotating and explains the occurrence of more significant strain rate. The trajectory of the contactnormal based fabric is not centered in the origin, due to the anisotropy in particle orientation generated during sample generation which is persistent throughout the shearing process. The sample sheared at a lower intermediate principal stress ratio (b = 0.0) has been observed to approach a smaller strain trajectory as compared to the case b = 0.5, consistent with a smaller fabric trajectory and less significant structural re-organisation. It also experiences less volume contraction with the out-of plane strain component being dilative.