The large-scale syntheses of global mean temperatures in IPCC fourth report suggested that the Northern Hemisphere temperature in the second half of the 20th century was likely the highest in at least the past 1,300 years and the 1990s was likely the warmest decade. However, this remains debated and the controversy is centered on whether temperatures during the recent half century were higher than those during the Medieval Climate Anomaly (MCA, AD 800–1300) and the Roman Warm Period (RWP, BC 200–AD 400), the most recent two natural warm periods of the late Holocene. Here the high resolution sea surface temperatures (SSTs) of two time windows around AD 990 (±40) and AD 50 (±40), which located in the MCA and RWP respectively, were reconstructed by the Sr/Ca ratio and δ 18O of Tradacna gigas shells from the northern South China Sea. The results suggested that the mean SSTs around AD 990 (±40) and AD 50 (±40) were 28.1 °C and 28.7 °C, 0.8 °C and 1.4 °C higher than that during AD 1994–2005, respectively. These records, together with the tree ring, lake sediment and literature records from the eastern China and northwest China, imply that the temperatures in recent decades do not seem to exceed the natural changes in MCA, at least in eastern Asia from northwest China to northern SCS.