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We investigated temporal changes in paddy rice phenology and yield under climatic and varietal changes in Shonai region, Yamagata Prefecture, northeast Japan across a period of 1982-2017. In the study region, the dominant variety shifted from Sasanishiki to Haenuki in mid 1990s. Temporal trends across the study period were significant in mean air temperatures for the months from May to July, and the temperature rise has accelerated heading, which was delayed by the varietal shift. We built models of the effects of climatic and varietal changes on phenological events and yield components: number of grains per land area, percentage ripened grains, and 1000-grain weight. Combining the yield component models, we built a yield model, with which we estimated the effect of the temperature rise from May to July on the yield. The temperature rise in May and June has reduced the yield by accelerating phenology, while that in July has increased the yield by raising 1000-grain weight. The net effect was no change in the yield across the study period, which, however, does not indicate an insensitivity of the yield to the temperature rise. Rather, the finding points to the dependency of the net change in the yield on seasonal pattern of the climate change. Climate change impacts on rice should therefore be quantified on the changes at monthly or shorter time scale rather than a seasonal mean. Our finding also points to the need to pay attention to the changes in agronomic practices such as varieties.