We used simulation by the reciprocity method to visualize the distribution of Green's function amplitudes in the source of a megathrust earthquake in the Nankai Trough and considered the effects of various areas (asperities or strong motion generation areas) on the simulated long-period ground motions at Konohana in the Osaka basin. We employed a fault source model proposed for an anticipated M9-class event in the Nankai Trough and the 3D Japan Intergrated Velocity Structure Model developed for simulations of long-period ground motions in Japan. Green's functions were calculated for about 1400 subsources by combining the finite-difference method and the reciprocity approach. Depths, strikes, and dips of subsources were adjusted to the shape of the upper boundary of the Philippine Sea plate. Ground motions with periods of 4-20 s were considered. The simulated distribution of peak amplitudes of Green's functions identified two strongly anomalous areas: (1) a large along-strike elongated area just south of the Kii Peninsula and (2) a parallel area closer to the trench. The elongation of the anomalies corresponded well with depth isolines at the top of the Philippine Sea plate. Postulating that plate shape influences simulated ground motions, we investigated the effect on Green's function amplitudes of phenomena related to plate shape: radiation pattern; variations of medium properties (e.g., velocity and density) at subsource depths; depth, strike, and dip; and the effect of soft sediments. We suggest that the cumulative effect on Green's function amplitudes of subsource radiation patterns, medium properties at subsource depth, reflection from crustal interfaces, and passage through soft sedimentary layers plays a critical role in the formation of amplitude anomalies. Analysis of waveforms and the time delay of peak amplitude demonstrate that large-amplitude waves of Green's functions in shallow parts of the plate boundary are composed mostly of surface waves.