Centennial-scale variations in the East Asian summer monsoon (EASM) remain ambiguous. In the present study, the δ18O of shells from the ostracode Bicornucythere bisanensis from Lake Nakaumi, Japan, were examined to identify the bottom salinity changes caused by EASM variations over the past 1700 yr. Four weak EASM periods were identified in Lake Nakaumi: at A.D. 600, 1000, 1350, and 1900. We detected discordance among the centennial-scale EASM variations in Japan and the δ18O of stalagmites (δ18Ostalagmite) in southern China. Furthermore, both total solar irradiance and atmospheric 14C concentration, which were previously considered to be linked with the centennial-scale EASM variations, were asynchronous with the EASM variations. Conversely, we observed significant positive and negative correlations between the EASM from Japan and the δ18Ostalagmite in north-central China, and the relationship was associated with the Asia-Pacific Oscillation (APO) index: centennial-scale EASM periods dominated during the high APO period. These synchronous variations imply that the strength of the EASM variations is tied to temperature gradients between East China and the north-central Pacific Ocean.