We successfully reproduced important features of long-period (7 to 8 sec), large-amplitude ground motions observed in the Yufutsu basin, Hokkaido, during the Mw 8.0 2003 Tokachi-oki, Japan, earthquake through numerical simulation of wave propagation. Recordings from the dense nationwide strong ground motion networks in Japan demonstrated significant spatial variation of long-period strong ground motions within the Yufutsu basin and revealed that the long-period shaking in the Tomakomai western port was the strongest of all the sites within the basin. In interpreting or predicting long-period strong ground motions in sedimentary basins, the importance of deep basin structures, such as the depth of bedrock with an S-wave velocity over 3 km/sec has been emphasized. However, the characteristics of the underground structure model of the Yufutsu basin that explain the observations indicate that thickness of near-surface (<1 km) soft sediments rather than bedrock depth governs the spatial variation of amplitudes of the long-period (7 to 8 sec) shaking in the basin. These findings suggest the importance of the detailed models of soft near-surface deposits as well as deeper basin structures such as bedrock depth for a better understanding of long-period strong ground motions in deep sedimentary basins.