We perform the UV deformation of the Green's function in free scalar field theory using a discrete heat kernel method. It is found that the simplest UV deformation based on the discretized diffusion equation leads to the well-known Pauli-Villars effective Lagrangian. Furthermore, by extending assumptions on the discretized equation, we find that the general higher derivative theory is derived from the present UV deformation. In some specific cases, we also calculate the vacuum expectation values of the scalar field squared in nontrivial background spaces and examine their dependence on the UV cutoff constant.