Modeling of generalized perfectly matched layer (GPML) absorbing boundary conditions in ground penetrating radar (GPR) simulation is discussed. Maxwell's equations are discretized by finite-difference time domain (FDTD) method,and Mur super absorbing boundary conditions and GPML absorbing boundary conditions are adopted to simulate GPR sections of a water-filled karst. GPR images of a multi-cylinder model and an inclined interface model are obtained by FDTD method with GPML absorbing boundary conditions. It shows that as an absorbing boundary condition GPML absorbs outgoing wave effectively. Its absorbing effect is better than that of Mur super absorbing boundary conditions. It can be applied to GPR simulations.