We investigated the geological structure below the Matsudai-Murono mud volcano, Tokamachi city, Niigata prefecture, Japan, using vertical distributions of S-wave velocities, estimated from surface wave inversion. From the surface to a depth of several meters, the S-wave velocity first increases, then decreases, and finally increases again. Below a depth of 10 m, there are two areas with high and low velocities in the horizontal direction. We found that the subsurface low-velocity layer is a mud layer produced by an eruption, and the deep low-velocity zone is a mudstone zone, some parts of which are transformed into soft clay by muddy water that drifts upward. The planar distribution of the S-wave velocity indicates that the deep low-velocity zone may be subdivided. The zone in which the velocity is particularly high corresponds to the area without surface uplift indicated by GPS; hence, this area is not influenced by the mud volcano. This study shows that it is possible to conduct subsurface geophysical investigations to clarify the eruption mechanism of the mud volcano.