The paper studies the effect of temperature (T), (T=300, 3200, 4000, 5000, 6000, 7000K) at pressure P=0GPa; pressure (P), (P=0, 100, 200, 300, 350, 400GPa) at T=7000K and thermal annealing time (t), t=47.8ps (after 105 steps) at T=7000K, P=400Gpa) on the structure of MgSiO3 bulk 3000 atoms by Molecular Dynamics (MD) simulation using Born–Mayer (BM) pair interaction potential and periodic boundary conditions. The structural results are analyzed through the Radial Distribution Function (RDF), the Coordination Number (CN), the angle distribution, size (l), total energy of the system (Etot) and the bonding lengths. The results show that the temperature and pressure had influenced the structural properties of MgSiO3 bulk and formation process geology of the Earth. In addition, the center of the Earth with T=7000K and P=350GPa has appearance and disappearance of the Si–Si, Si–O, O–O, Si–Mg, O–Mg, Mg–Mg bonds and SiO4, SiO5, SiO6, MgO3, MgO4, MgO5, MgO6, MgO7, MgO8, MgO9, MgO10, MgO11, MgO12 angle distributions. When increasing the depth of the Earth’s surface (h) lead to size (l) of MgSiO3 decreases, total energy of the system (Etot) increases, position of first peak of Radial Distribution Function (RDF) is (r), height of RDF is g(r) varies greatly with h from h=0km to h=1820km, gradually decreasing with h from h=2000km to h=3200km and the smallest structural change with h>3200km that shows has influence affects on the geological formation of the Earth.