AbstractThe carbon isotope (δ13C) in marine biogenic carbonate is a valuable tool for comprehending the marine carbon cycle. However, the absence of monthly resolved δ13C records before the instrumental era (since 1850) hinders us to fully understand the global carbon cycle. In this study, we present a δ13C record from a modern Tridacna gigas shell (δ13Cshell) collected from the southern South China Sea (SCS) with an average resolution of ∼10 days. The δ13C record illustrates seasonal and interannual cycles which are superimposed by long‐term decreasing trend. We investigate the environmental controls influencing the δ13Cshell on different time scales. We suggest that more positive δ13Cshell values observed during the juvenile stage (first 8–10 years), which correspond to a high growth rate, can be attributed to 13C enrichment of the internal dissolved inorganic carbon pool. This resulted from the exponential increase of symbiotic zooxanthellae, and preferential 12C sequestration by the accelerated buildup of productive tissues. On the interannual time scale, changes in δ13Cshell were likely affected by both internal (vital effect) and external processes (sea water δ13C), as well as being disturbed by the super El Niño‐La Niña event. Seasonal changes of δ13Cshell were mainly dominated by the intensity of photosynthesis and respiration of symbiotic zooxanthellae, which depend on the seasonal solar irradiance variations in association with precipitation and the South Asian summer monsoon. Our study sheds light on the controlling factors of δ13Cshell variations on seasonal timescale and the long‐term trend, providing insight into the carbon cycle over geological history.