The seabed response under wave loading is important for the stability of foundations of offshore structures. Unlike previous studies, the wave-induced seabed response in a spatially random porous seabed is investigated in this study. A stochastic finite element model which integrates random field simulation of spatially varied soil properties and finite element modeling of wave-induced seabed response is established. Spatial variability of soil shear modulus, soil permeability, and degree of saturation, are simulated using the covariance matrix decomposition method. The results indicate that the pore water pressure and stress distribution in the seabed are significantly affected by the spatial variability of the shear modulus. The mean of maximum oscillating pore pressure in a randomly heterogeneous seabed is greater than that in a homogenous seabed. The uncertainty of the maximum oscillating pore pressure first increases and then reduces with the correlation length. The effects of spatial variability of permeability and degree of saturation are less significant than that of shear modulus. The spatial variability of soil permeability increases the uncertainty of oscillating pore pressure in the seabed at shallow depths. The spatial variability of shear modulus and degree of saturation affects the uncertainty of oscillating pore pressure of the whole seabed.