There is a regional variation of seismicity in the Japan trench region characterized by cluster distribution of seismically active zones which persist for at least a few decades. We conducted seismic refraction-reflection experiments there to clarify the relationship between seismicity and crustal structure. A velocity structure model was obtained by travel-time inversion. Although there does not seem to be distinct relationship between seismicity and the bulk velocity structure, we found a good relationship between seismicity and variation of reflective amplitude. Large amplitude reflected waves generated at the plate boundary were observed at low seismicity region and vice versa.