Correlation between structure and dynamics of GeO2 system under compression is investigated by molecular dynamics and Monte-Carlo methods. Results show that structural phase transition occurs at the range of oxygen packing factor from 0.55 to 0.60. Self-diffusion coefficient of Ge and O exhibits anomalous and depends on percentage of GeOx polyhedrons (x = 4,5,6) and packing factor/ free volume of model. The self-diffusion coefficient can be determined via percentage of GeOx units and free volume fraction. The data mining technique is applied to clarify the polyamorphism, structure and dynamics heterogeneities. The cause of anomalous diffusion has been elucidated.