The time-dependent mild-slope equation (MSE) is a second-order hyperbolic equation, which is adopted to consider the irregularity of waves. For the difficulty of directly solving the partial derivative terms and the second-order time derivative term, a novel mesh-free numerical scheme, based on the generalized finite difference method (GFDM) and the Houbolt finite difference method (HFDM), is developed to promote the precision and efficiency of the solution to time-dependent MSE. Based on the local characteristics of the GFDM, as a new domain-type meshless method, the linear combinations of nearby function values can be straightforwardly and efficiently implemented to compute the partial derivative term. It is worth noting that the application of the HFDM, an unconditionally stable finite difference time marching scheme, to solve the second-order time derivative term is critical. The results obtained from four examples show that the propagation of waves can be successfully simulated by the proposed numerical scheme in complex seabed terrain. In addition, the energy conversion of waves in long-distance
wave propagation can be accurately captured using fast Fourier transform (FFT) analysis, which investigates the energy conservation in wave shoaling problems.