This review represented some topics for molecular dynamics (MD) simulation, i.e., the initial conditions, algorithms, empirical potentials, and thermodynamic ensembles, and their application in simulation of glass materials. The methodologies of structural analysis and property calculation of glass materials were summarized. Recent development on the MD simulations of glasses, such as the structure model of oxyfluoride glass, the design of glass ceramics with target crystal phase, the prediction of compositional-dependent crystallization phase evolution and crystalline phase transformation via simulation of phase separation, optimization of the luminescent performance of glass ceramics, and improvement of the mechanical strength of aluminosilicates glass were represented. In addition, three future research directions were also prospected, i.e., the parameters of the simulation system to improve the accuracy of the results, the potential function with the help of first-principles molecular dynamics, and the practicability of the simulation with combining other methods.