The detailed P-wave velocity structure of the surface layers in the sea area off Kyushu, Japan, was analyzed using a three-dimensional (3-D) tomographic method for explosion seismic refraction and reflection surveys. Approximately 1,830 P-wave arrival times received from 15 rounds of explosion seismic surveys were used in the structural analysis of the two-dimensional (2-D) profile. The 3-D pseudo-bending technique, which is a fast algorithm for two point ray tracing, is used in forward modeling. The conjugate gradient (CG) algorithm was used to solve the discrete linearized equation of the travel-time residuals. The velocity structure obtained from the tomographic technique indicates heterogeneity in the lateral and vertical directions for seismic waves within in the study area. The sedimentary layer is thin near the coast and thickens gradually off the coast. The boundary contours of sedimentary layers reveal complicated serpentine curves. Lateral and/or vertical convex and concave structures are prominent in the contours. The scales of some concave and convex anomalous velocity structures are small; anomalous structures on a 10-m scale were identified. This might imply that a high resolution tomography imaging technique can be introduced in shallow-structure surveys. The explosion seismic survey tomographic technique characterizes the complicated structure, geometry and physical properties of abnormal objects well, and tomographic inversion of the explosion survey is available for detailed geological structure surveys and resource explorations, especially for resources such as oil, gas and minerals in complicated geological conditions. The calculated convergence velocity and stability of the tomography technique are also of a high standard.