The great kinetic energy of penetration can cause damage to the structure. It is important to the protection engineering that predicting the penetration damage effect of the underground caverns accurately. In order to solve the problems of current method, an improved IGWOLSSVM model is put forward. This model can form a mapping relationship between inputs and outputs by training the training samples. It can get corresponding peak pressure of the vault according to the inputs, and predict damage effect of the underground caverns with different spans and different burial depths. The results of ANSYS/LSDYNA numerical simulation show that the model has good prediction effect on penetration effect of the underground caverns, which can meet the engineering requirements.