Anthropogenically induced global climate change greatly threatens biodiversity and functions of various types of ecosystems. Quantitative prediction of the climate-related effects is urgently required for the conservation and management. Taking into account the sensitivity to thermal stress and water-level change, the rocky intertidal ecosystem is an ideal model for the study of global climate change effects. This study aims to evaluate heat stress using a data logger, and to examine how heat stress is related to variation in rocky intertidal communities. We deployed data loggers on intertidal rock surfaces of 25 census plots of rocky intertidal community established at five shores in each six regions along the northwestern Pacific coast of Japan. Daily maximum rock temperature varied between 27.2 °C in the southern Hokkaido (42 °N) to 47.4 °C in the southern Kagoshima (31 °N). Regression analyses on heat stress and abundance of rocky intertidal organisms revealed that the coverage of encrusting algae is positively correlated with, and that of erected algae negatively correlated with heat stress. The obtained results can be used as a baseline for anticipating the future changes in community structure with ongoing global climate changes.