Previous studies on surface temperature reconstructions for the last 2000 years (2 k) revealed a long-term cooling trend for the last millennium in comparison to the previous millennium. However, knowledge on the decadal- to centennial-scale variability in sea surface temperature and the underlying governing mechanisms throughout the period is limited. We reconstructed high-resolution continuous sea surface temperature changes over the last 2 k in the northwest Pacific margin based on the alkenone unsaturation index. Our alkenone temperature record revealed enhanced and more rapidly changing climate variability during the last millennium (approximately 1200–1850 Common Era) than during the previous millennium. Cold and hot extremes also occurred more frequently during the last millennium. The enhanced and rapidly changing climate variability appears to be associated with frequent volcanic eruptions and grand solar minima. The reconstructed surface temperature variability tends to be associated with variations in the East Asia summer monsoon and the Pacific Decadal Oscillation, implying that these variations are also enhanced in the last millennium than in the previous millennium.