In this study, we simulated the structural transformation and self-diffusion mechanism in liquid GeO<sub>2</sub> oxide system. Under compression, structure of liquid GeO<sub>2</sub> model tends to transform gradually from low-density phase to high-density phase. Concentration of basic structural units can be determined via density of material model. The average Ge-O bond distance in GeO<sub>4</sub> tetrahedra is smaller than the ones in GeO<sub>5</sub> pentahedra and GeO<sub>6</sub> octahedra. Each GeO<sub>x</sub> polyhedron always exists a Ge-O bond with the longest length (the weakest bond). The diffusion mechanism in liquid GeO<sub>2</sub> Oxide system is via the breaking the weakest bonds that accompanying the change local coordination environment of Ge cations. The longest Ge-O bond in a GeO<sub>5</sub> pentahedron is very weak in comparison to the one in other polyhedra. The diffusivity is significantly dependent on the number of GeO<sub>5</sub> pentahedra. The increase of GeO<sub>5</sub> under compression is the origin of anomalous diffusion in liquid GeO<sub>2</sub> oxide. The increase of average Ge-O bond distance under compression is also clarified in this work.