The regional paleoenvironmental record of Tokyo, central Japan, is required to enrich our understanding of climate change in East Asia and its impact on Japanese civilizations. Previous studies have generated paleotemperature records based on the analysis of shell mounds along the coast of Tokyo Bay and pollen from terrestrial borehole cores. However, a continuous, high time-resolution, quantitative paleotemperature record does not exist. A piston core was recovered from Tokyo Bay from which 22 mollusk shells were extracted. An age model for the core, determined via accelerator mass spectroscopy (AMS) 14C dating of the shells and a scoria layer from the Hoei eruption (1707 CE), showed that the core contains continuous record from ca. 2400 BCE. We analyzed the alkenone unsaturation ratios (UK’ 37 ) to reconstruct the variations in the paleotemperature. The temperature during the Meghalayan was generally warmer than that at present exhibiting a declining trend, which roughly matches the changes in the orbital-forcing summer insolation and the millennial-scale latitudinal shift of the subarctic front in the northeastern Pacific Ocean. The largest cold period, which occurred ca. 2300 BCE and had a minimum temperature of 19.5 °C, interrupted the warm conditions. This cold period may correspond to the global cooling/drying “4.2 ka BP event,” which marks the boundary between the Northgrippian and Meghalayan. Our results also revealed that several cold periods occurred, which may have been caused by decreases in solar activity or large volcanic eruptions. Particularly, large decadal to centennial-scale cold periods were observed ca. 440 BCE and 100 CE during the Yayoi era (ca. 900 BCE–300 CE). The coldest period after the establishment of a centralized system of government (ca. 300 CE–present) was recorded ca. 1050 CE, which may have been caused by the combination of a strong El-Niño mode and reduced solar activity. These climate change events can all be linked and, therefore, may be the potential causes of significant periods of famine and civil war in Japanese history, which eventually led to major shifts in Japanese social systems.