El Niño-Southern Oscillation (ENSO) is a major driver of climate variability and is known to have profound impacts on weather patterns worldwide. While the modern era is well documented, less is known about ENSO variability during the pre-industrial period. Here, we use a high-resolution speleothem oxygen isotope record from Hulu Cave, China, to reconstruct tropical Pacific sea surface temperature (SST) variability during the past millennium. Our results indicate that El Niño events were more frequent during the Medieval Climate Anomaly (MCA) than during the Little Ice Age (LIA), and their magnitudes were larger during the early-LIA than the late-LIA. These findings suggest that the MCA and LIA experienced distinct ENSO variability, which may have contributed to the different climatic conditions during these periods. Our data provide valuable insights into the natural modes of ENSO variability over multiple centuries and have important implications for understanding the future response of ENSO to global change.