In this work, the through silicon via (TSVs) with 100 μm × 13 μm depth-to-width ratio after 300°C and 400°C annealing treatment were characterized respectively by electron backscattered diffraction (EBSD). Finite element modeling was used to demonstrate the Von Mises mechanical stress distribution of copper in TSV caused by different thermal expansion coefficient of copper and silicon at different temperature. According to the modeling results, the compressive yield strength of copper in our experiment is about 1 GPa. The Schmid factors results analyzed from EBSD data show the Schmid factors of copper grains in TSV are almost all larger than 0.3 and soft orientation both before and after annealing treatment. According to Schimd law, the plastic deformation occurs in the grains that have the highest Schmid factors. Schmid factor distribution in the range of 0.45–0.5 reduces in copper after 400°C annealing treatment. The textures of the as deposited copper are eliminated by the migration of 38.9°/110 twist boundaries mainly composed by Σ9 in both annealing treatments. Annealing at 400°C makes the deposited copper contains more 60°/111 coherent twin Σ3 boundaries that have lower energy than that of the copper annealed at 300°C.