In order to explore the cause and mechanism of water damage on asphalt pavement, the finite element software ABAQUS was used, combined with the pavement structure combination of Yinzhou Lake Expressway in Guangdong Province, and based on the seepage theory, the finite element models under the three working conditions of conventional water concentration field, actual non-uniform water concentration field and comprehensive consideration of actual non-uniform water concentration field and saturated liquid water were established respectively. The mechanical response of pavement under different working conditions was analyzed. The results show that the actual presence of non-uniform water vapor concentration field increases the cracking risk of the upper layer. With the intervention of liquid water caused by rainfall, the surface layer is in the alternating positive and negative pore water pressure, repeatedly scour the fatigue cracking site, further accelerating the stripping of asphalt and aggregate, and finally leading to water damage related diseases. The upper layer is subjected to the most serious void water pressure. Emphasis should be placed on enhancing the water damage resistance of the upper layer.