<p>Coral reefs play a critical role in the global carbon cycle by acting as significant carbon sinks, and they are able to sequester both inorganic and organic carbon. To resolve the methodological challenge of partitioning inorganic and organic carbon fluxes in coral reef ecosystems, we developed an integrated framework combining in-situ reef carbonate budgets (ReefBudget), satellite-derived net primary production (vertically generalized production model (VGPM)), and literature data. Five stations were set up across three distinct South China Sea regions: the relatively pristine Xisha Islands, moderately disturbed Sanya Bay, and Miaowan Island near Guangdong. Carbon fixation patterns exhibited clear spatial variability in the study sites. The Xisha Islands stations demonstrated the highest sequestration rates, with organic carbon fixation reaching 1 090.9 t C/(km²·a) and inorganic carbon fixation 537.3 t C/(km²·a). In contrast, anthropogenically disturbed nearshore sites such as Miaowan Island showed significantly reduced organic carbon fixation (405.4 t C/(km²·a)) and net inorganic carbon loss (−49.4 t C/(km²·a)). This integrated approach represents a methodological improvement over conventional carbonate system proxies or skeletal growth indicators, offering a more comprehensive assessment of reef carbon dynamics. While current estimates carry an uncertainty margin of approximately 46%, they provide crucial baseline data for regional-scale carbon budget modeling. To improve the precision, future validation shall incorporate systematic measurements of both water-column and benthic net community calcification/production rates, along with detailed species data.</p>