The complicated effects of climatic and environmental conditions on coral δ13C have hindered its use as a universal proxy for biological activity and climate change. Changes in annual resolution δ13C levels from the South China Sea (SCS) were studied to explore the biological and climatic significance of coral δ13C during the mid-Holocene. The growth-rate-related kinetic isotope effect on modern coral δ13C may be limited, site- and/or colony-specific. Furthermore, coral δ13C and sea surface temperatures (SST) are inversely related, but their correlation is weak. These results suggest the influence of complicated controlling factors on modern coral δ13C. As for the mid-Holocene corals, no obvious growth-rate-related kinetic isotope effect has been found in their coral δ13C series, and the effect of solar irradiation on coral δ13C is difficult to directly evaluate for the low resolution of reconstructed solar records and the dating errors. However, mid-Holocene coral δ13C series show temperature-dependent changes over the studied periods during 6100–6500 yr BP. The significant negative correlation between coral δ13C and SST has been attributed to the high SSTs during the mid-Holocene. This is based on the observation that coral δ13C and the photosynthesis to respiration ratio (P/R) are usually positively related, but P/R is significantly and negatively related to temperature under high temperature conditions in that photosynthetic activity of heat-stressed corals will drastically reduce due to the decreases of population density and photosynthetic rate of the zooxanthellae. •Suess effect and global warming lead to negative correlated modern coral δ13C-SST.•Mid-Holocene coral δ13C shows temperature-dependent changes.•Negative correlated fossil coral δ13C-SST is a response of coral to thermal stress.