Temperature seasonality, the difference between summer and winter temperature, has significant influences on global terrestrial and marine ecosystems. However, most of proxy-based climate records are of limited temporal resolution and thus insufficient to quantify the past temperature seasonality. In this study, high-resolution Sr/Ca ratios of modern (live-caught) and fossil (dead-collected) Tridacna gigas shells from the South China Sea (SCS) were used to reconstruct the seawater temperature seasonality during the late Holocene. The averaged seawater temperature seasonality around 2165 ± 75 BC (4.46 ± 1.41°C, derived from the data of 18 yr) were similar to the seasonality of recent decade (4.41 ± 0.82°C during AD 1994–2005), but the temperature seasonality around AD 50 ± 40 (3.69 ± 1.37°C, derived from the data of 48 yr) and AD 990 ± 40 (3.64 ± 0.87°C, derived from the data of 11 yr) was significantly lower than that during AD 1994–2005. The reduced seasonality around AD 990 ± 40 was attributable to the unusually warm winter during the medieval times, probably caused by the weakening of East Asian Winter Monsoon. Our study highlighted the potential of T. gigas shells in providing high-resolution seasonality climate information during the late Holocene.