The 3-D surface wave Boundary Element Method is applied to the same set of strong motion records as those of Part 1 (Kato et al., 1993), namely, the long-period strong motion with periods around 8 sec recorded at the JMA (Japan Meteorological Agency) stations in Yokohama and Tokyo during the 1980 Izu-hanto-toho-oki earthquake. This method simulates exact Love and Rayleigh waves in a laterally heterogeneous medium including 3-D basin structures. The needed computer memory and CPU time are made manageable by assuming the inside and outside of the basin to consist of horizontal flat layers. In addition, vertical interfaces are assumed between the basin and the outside bedrock for simplicity in this study. After checking the range of validity of the flat-layer approximation for the Kanto sedimentary basin, the generation and propagation of surface waves in the basin are numerically investigated. In particular, our investigation places special emphasis on the cause of the observed long duration, which could not be explained in Part 1 using the surface wave Gaussian Beam method. When the bedrock outside the western margin of the Kanto basin is incorporated into the model, the observed long duration at the Tokyo station is successfully reproduced. This can be explained by the strong surface waves generated by the surface wave to surface wave conversion at the margin and appearing in Tokyo after the direct surface waves from the epicenter. This result agrees with Kinoshita et al. (1992), who studied records from an array of seismographs in Tokyo. Moreover, when a sedimentary basin of Sagami Bay is included as was done in Part 1, the simulations are greatly improved, particularly at the Yokohama station, which corresponds to the node in the radiation pattern of the source. This is due to the fact that the radiation pattern is strongly affected by the near-source heterogeneity of the Sagami basin. All these results, together with direct comparisons to 2-D modelings, clearly show the strong 3-D effects of the basin structures on the generation and propagation of surface waves for this earthquake.