An analysis method of a composition network topology structure includes obtaining a three-dimensional body for analysis capable of being used for three-dimensional measurement of a concentration distribution of a specific element contained in a sample within a predetermined measurement range. The three-dimensional body for analysis is divided into unit grids composed of a plurality of finer three-dimensional bodies. An amount of the specific element contained in each of the unit grids is obtained. Maximum-point grids respectively having a largest amount of the specific element among adjacent unit grids are obtained. The composition network topology structure of the specific element owned by the sample is quantified in relation to the maximum-point grids contained in the three-dimensional body for analysis.