The structure size of the crater formed by the earth-penetrating nuclear bomb explosion is one of the important parameters for evaluating the earth-penetrating nuclear bomb damage power. Obtaining the structure size of the crater formed by the earth-penetrating nuclear bomb explosion with different yields is great significance for the evaluation and design of the nuclear bomb damage power. In this study, considering the contradictory relationship between the structure size of the earth-penetrating nuclear bomb and the structure size of the equivalent TNT mass, we propose to use the equivalent energy mapping method to realize the finite element numerical simulation of the earth-penetrating nuclear bomb exploding into craters analyzed and compared the simulation results with the structure size of the crater formed by the ESS nuclear bomb explosion in the United States. The analysis results show that the error between the simulated crater radius and the real crater radius is 3.26%, and the error between the simulated crater depth and the real crater depth is 28.57 %. It meets the calculation accuracy error range of crater formation from nuclear explosion to chemical explosion. Therefore, this method provides an effective numerical simulation method and a means of obtaining the structural size data of the explosion crater for the earth-penetrating nuclear bomb cratering.