Representation on the variation of Earth system phenomenon is important to Earth System Science research. However, owing to the complexity and unnecessary transformation, mathematic models are not good method to represent the variations of earth system phenomena. Grid-based models can overcome the shortcomings well. But the grid in used is not perfect enough. A three-dimensional (3D) Global Spatial Grid (GSG), named SDOG-ESSG, was adopted to represent the 3D and large-scale earth system phenomena. The models of variation representation was proposed, and the experiment on ionosphere was taken to prove the superiority of the methods.