The objective of the work is to numerically study the meso-scale deformation of amorphous glassy polymer. A molecular polymerization algorithm is employed to generate three-dimensional (3D) random networks of polymer, in which the micro-parameters and meso-structures, such as entanglement point, sliding point, etc. are considered. Then, 3D unit cell model and finite element method are used to calculate the stress and deformation relations of polymer. The evolution of meso-structure of glassy polymer with deformation is obtained simultaneously. Further, variation of the orientation of polymer chain with deformation was quantitatively studied.