Three-dimensional crustal structures in and around the Japanese Islands were calculated from gravity data. In this calculation we adopt the crustal structure along the Oga-Kesennuma line, obtained from explosion seismological observation, as a constraint. Gravity anomalies employed in this study is the Slab Residual Gravity Anomaly, which is computed by removing gravity contribution arising from subducting plates from the observed gravity anomalies. For computational ease, we divided the Japanese Islands into five blocks; Hokkaido, Tohoku, Chubu, Shikoku-Chugoku and Kyushu. In each block, we generated cross sections of gravity anomalies along latitudinal and longitudinal directions with 20 arc-min intervals. Two-dimensional Talwani’s method was applied to estimate density model structures. For each block, we applied the following steps. At first, we estimate a density model along profiles in latitudinal direction, and then estimate along profiles in longitudinal direction. We repeated these steps until crustal structures beneath cross points merged into some stable values. Combining structures calculated for adjacent blocks, we draw a three-dimensional distribution of surface layer, Conrad and Moho discontinuities. The crustal structure thus estimated was generally concordant with both existing explosion seismological and inversion crustal models, but at the same time showed some significant differences in intermediate scales.