A permeable seabed may influence the evolution of an internal solitary wave propagating on a continental shelf and nearshore. In order to study the porous effect, numerical simulations are performed to investigate the flow field and waveform inversion of a large depression ISW propagating over a porous trapezoidal obstacle. A finite volume based Cartesian grid method is adopted to solve the Reynolds averaged Navier-Stokes equations using a k-ε model for the turbulent closure and porous media model together. Numerical results reveal that waveform inversion weakens significantly, as the porosity of the obstacle increases, except when porosity nf<0.2. At the same time, the magnitude of vorticity and turbulent energy decrease remarkably due to acute reduction of the production term induced by percolation and wave-pore interaction. Moreover, a skewed hump shaped relation appears between the maximum vorticity and the porosity. For transmitted wave energy on a horizontal plateau, total energy may decrease as nf<0.2 but increases moderately while nf>0.2 during a strong wave-obstacle interaction.