In this article, the dissipative dynamical evolution method based on the discrete variational principle is applied to a three-dimensional (3D) vesicle system. The stationary shapes of vesicles are obtained through the minimization of membrane bending energy without any symmetric assumption, which is an outstanding merit of our method. Aiming at a 3D vesicle system with certain parameter settings, a series of axisymmetric shapes are achieved by our method. The simulation results are in good agreement with those obtained with axisymmetric assumption, which indicates that our method can describe the deformation of 3D vesicle with extremely high precision. In addition, a shape transition between two stable states with great difference is studied, which further implies the capability of our proposed method in simulating large deformations regarding the 3D membrane. We believe that we have provided a very powerful simulation method for the future studies of bio-membrane deformations.