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Accurately and effectively handling undulating interfaces, including both free surfaces and internal interfaces, remains a key challenge in seismic exploration. Traditional scalar wave equations typically neglect the influence of internal interfaces on wave propagation. To address this, the wave equation in layered media (WEILM) is established by introducing the Dirac delta function. For undulating interfaces, existing methods are mostly grid‐based, and often require additional grid processing to achieve accurate description, which increases computational cost. Therefore, by introducing the meshless method combined with free surfaces boundary conditions, this article proposes the method for dealing with undulating surfaces on the basis of the radial‐basis‐function‐generated finite difference (RBF‐FD) method. Theoretical analysis indicates that the stability of the proposed method is affected by the sum of the stencil node weights. Numerical experiments show that, compared with the scalar wave equation, the interfaces term introduced in WEILM effectively adjusts waveform amplitudes. Moreover, relative to the classical Lax–Wendroff correction (LWC) method, our approach can avoid spurious diffraction waves caused by grid discretization when handling undulating surfaces. By applying RBF‐FD to solve WEILM in conjunction with the method for dealing with undulating surfaces, complex seismic wavefield, including undulating surfaces, can be simulated with higher accuracy.