In order to study the damage characteristics and mechanism of underground water on underground structure, factors of structure deformation and cracks based on a case study had been investigated. Meanwhile, finite element method had been used to simulate the deformation and decrease of stiffness. And structure deformation mechanism had been investigated, together with cracks characteristics and the effect on the structure’s safety. It was found that the underground structure would be swollen up and floated as the float was larger than the structure’s weight. And the uptrend of boundary retaining wall was restrained by soil, which made vertical displacements in columns and concrete walls different and resulted in structure cracks and the decrease of structural stiffness. The general structural damage was depended on the plan size and controlled by the short side. And the damage was more serious in central than that in boundary.