Molecular dynamics (MD) simulation is applied to investigate the structural characteristics of Al2O3–SiO2 system with the Al2O3 content at 60 mol.% (Mullite — 3Al2O3⋅2SiO2). MD models containing 5250 atoms in cubic box with periodic boundary conditions are constructed at 3500 K in 0–100 GPa pressure range. The Born–Mayer–Huggins potential is applied in this study. Based on the cluster analyzes and MD data visualization technique, the structural characteristics of Mullite melt, such as the short-range and intermediate-range order, the local environments of oxygen and network structure will be clarified. Under compression, the Al–O bonds are broken, leading to incorporation of Al atoms into Si–O subnet through both nonbridging oxygen (NBO) and bridging oxygen (BO), forming –Al–O–Si-network (Al–O–Si, Si–O–Al2, Si2–O–Al, Si–O–Al3, Si2–O–Al2 and Si3–O–Al). The degree of polymerization (DOP) of the silica network and alumina network increase with pressure and the DOP of SiOx-network is lower than that of AlOx-network under compression. The statistics of corner, edge and face-sharing bonds between two adjacent TOx units (T is Si, Al; x = 3–7) as well as characteristics of all type OTy linkages (y = 2–6) are investigated in detail. Structural and compositional heterogeneities are clarified via analysis of structure and size distribution of TOx-clusters.