The existence of rugged free-surface three-dimensional tunnel conditions in the coal seams, caused either by geological or mining processes, will inevitably influence wave propagation characteristics when the seismic waves go through the coal mines. Thus, a modified image algorithm has been developed to account for seismic channel waves propagating through this complicated topography with irregular free surfaces. Moreover, the seismic channel waves commonly exhibit damped and dispersive signatures, which is not only because of their own unique sandwich geometry of rock–coal–rock but also because of the viscoelastic behavior of coal. Considering the complexity of programming in three-dimensional tunnel models with rugged free surfaces, an optimized vacuum grid search algorithm, enabling to model highly irregular topography and to compute efficiently, is also proposed when using high-order staggered finite-difference scheme to simulate seismic channel wave propagations in viscoelastic media. The numerical simulations are implemented to investigate the accuracy and stability of the method and the impact of coal's viscoelastic behavior on seismic channel wave propagation characteristics. The results indicate that the automatic vacuum grid search algorithm can be easily merged into high-order staggered finite-difference scheme, which can efficiently be applied to calculate three-dimensional tunnel models with rugged free surfaces in the viscoelastic media. The simulation also suggests that the occurrence of a three-dimensional tunnel with free surfaces has a remarkable influence on the seismic channel wave propagation characteristics and elastic energy distribution.