The El Niño-Southern Oscillation (ENSO) is the principal climatic system in the modern Pacific Ocean, and it potentially influences the global climate. The South China Sea (SCS), in the western tropical Pacific, is significantly affected by ENSO activity. We have conducted a high-resolution oxygen isotope study of the shells of one modern and four fossil Tridacna from the Xisha Islands in the SCS. The results for the modern sample reveal that the shells of Tridacna are a good proxy of ENSO variability. We used the results of the oxygen isotope composition of four fossil Tridacna to produce high-resolution records of ENSO activity during four time slices in the Holocene. The results indicate that ENSO variability in the early Holocene was comparable to that of today, and that a minimum in the frequency and intensity of ENSO activity occurred in the mid Holocene. These findings are consistent with paleoclimatic results from corals, mollusks and sedimentary records. However, the observed extremely low frequency and moderate ENSO intensity at 4.7 ka indicate an anomalous pattern of ENSO changes within this interval of climatic transition. In addition, seasonal temperature variations during the Holocene were different from those of today and extreme seasonality may also occur during warmer periods.