An overset mesh-free finite-difference method (OM-FDM) is proposed for two dimensional (2D) time domain seismic wave modeling using second-order elastic displacement wave equations in a generally isotropic medium that exhibits complex surface topography and subsurface structures. The complex surface topography was discretized using an overset mesh-free node generation method, thus arranging surface nodes on the surface topography naturally and outperforming the Cartesian grid in terms of geometric flexibility. A Cartesian grid was employed to discretize the total computational region in terms of computational efficiency. The QR-decomposition radius-basis-function finite-difference method (QR-RBF-FDM) and finite-difference method (FDM) were adopted to solve the equation independently in the mesh-free node and Cartesian grid. The data transfers between them were conducted through QR-RBF interpolation to facilitate mesh-free calculation, thus eliminating the requirement for node-to-grid matching. The improved free surface boundary condition was implemented in the QR-RBF-FDM. Furthermore, a more appropriate formula for the outward normal direction was developed. The numerical solutions of the proposed method were compared with those of the curvilinear grid FDM and standard FDM to verify the effectiveness of the proposed method. The results indicate that the proposed method avoids numerical scattering induced by staircase approximations of Cartesian grids, while saving a considerable amount of computational cost. This method is likely to be a better candidate than the mesh-free FDM for seismic numerical simulation with free-surface topography.