Seasonal climate variability is an important component of Earth's climate system, and has a significant impact on ecosystems and social systems. However, the temporal resolution of most proxy-based paleoclimate records is limiting to fully understand the past seasonal changes. Here, we used high-precision monthly resolution Sr/Ca records of three Tridacna squamosa specimens from the northern South China Sea (SCS) to reconstruct the sea surface temperature (SST) seasonality during three time periods from the middle Holocene. The results suggested that SST seasonality in the northern SCS during the middle Holocene (3.21 ± 0.98°C) was smaller than that for recent decades (AD 1994–2004, 4.32 ± 0.59°C). Analysis of modern instrumental data showed that the SST seasonality in the northern SCS was dominated by the winter SST, which was deeply influenced by the intensity of East Asian winter monsoon (EAWM). A strong EAWM usually resulted in cooler winter SST and a larger SST seasonality in the northern SCS. The reconstructed Holocene EAWM records showed that the EAWM strengthened from the middle to late Holocene, which was seen in our reconstruction of less SST seasonality changes during the middle Holocene in the northern SCS. This study highlighted that the Sr/Ca ratios from Tridacna shells can be used as a potential high-resolution indicator of past seasonal climate changes.