Three sets of original dynamics model parameters for MgO–Al2O3–SiO2 (MAS) system were reported for the first time in this paper; moreover, a new parameter optimization standard was put forward to study three different molecular dynamic models of MAS glass-ceramics. The limitations of the conventional parameter optimization methods were also studied. The results indicate: (i) Born-Mayer-Huggins (BMH) model can be only used to simulate amorphous MAS systems. Furthermore, both static optimization and a dynamics test are necessary; (ii) for structure optimization or macroproperties calculation, high accuracy has been achieved relative to the experimental results by using the core-shell (CS) model; (iii) partialQ model computes at a high speed, about twelve times that of the CS model; (iv) for a bulk system, the partialQ model can be first used to obtain an initial structure rapidly, followed by the CS model for high accuracy calculation. In this way, both accuracy and efficiency are achieved. When the model was used to simulate the cordierite crystal and the amorphous in the cordierite glass-ceramic, the results were consistent with the experiments and the structure data from the ab initio calculation. Simulations on amorphous structures in the cordierite glass-ceramic with various compositions displayed that the bond length or coordination numbers (CN) of Si–O and Al–O remained the same with increasing content of MgO, suggesting no change in the tetrahedral configuration of short-range structure. Although the bond length of Mg–O stays almost the same with the increasing content of MgO, the coordination number increases to a certain extent, and the content of O-bridge in SiO2 glass drops from 100%–60% in pyrope glass.