To investigate the self-diffusion mechanisms of atoms in forsterite in supercooled liquid state, we performed molecular dynamics calculations. The results show that the atoms migrate with jumps from a stable site to an adjacent site. From analyses of the stress auto-correlation function (SACF) and mean square displacement (MSD), we determined the viscosity and self-diffusion coefficients. Furthermore, it was found that the jumping probabilities of Mg and Si, which are located at positions with high Si densities, are higher than the averaged probability, because of a structural distortion of surrounding SiO₄ units with strong Si–O bonds. The mechanisms of self-diffusion are important to understand the phase transition dynamics of natural forsterite in proto-planetary disks and interstellar molecular clouds.