Cyclical ontogenetic changes of shell microstructures have been observed in the subfamily Anadarinae (Mollusca: Bivalvia, Arcidae) including fossil taxa. The changes in the bloody clam Scapharca broughtonii are controlled by temperature, which fluctuates seasonally, and can be used to determine the age of the individuals and to reconstruct paleoenvironments. In this study, samples of S. broughtonii from eight localities covering broad geographical regions at various latitudes in Japan, Korea, and Russia were examined to assess the utility of time series variations in microstructures for paleoenvironmental and paleoecological studies. All specimens showed cyclical changes in the relative thickness of the composite prismatic and crossed lamellar structures in the outer layer with ontogenetic progression, and thus, this feature can be used as a proxy for water temperature of their habitats. Specimens from southern latitudes showed higher annual shell growth rates than northern specimens, suggesting that low temperatures arrest shell growth in S. broughtonii and play a key role in determining the longevity and body size in S. broughtonii. In long-lived individuals from the four northernmost localities, the relative thickness of the composite prismatic structure tended to decrease as the individuals aged, which may be a consequence of declining physiological activity, such as organic matrix secretion.