The carbon cycle in coral reefs, one of the most productive ecosystems in the ocean, includes the combination of organic carbon metabolism (photosynthesis/ respiration) and inorganic carbon metabolism (calcification / dissolution). The photosynthesis of plants in coral reefs converts CO2 into organic carbon, making a useful supplement to organic carbon cycle. Because of the highly efficient organic carbon cycle facilitated by coral reef animals′ feeding activities and micro\|biological degradation, there are no more than 7% of organic carbon being precipitated into sediment. While the horizontal flux of organic carbon transported into ocean is greatly controlled by hydrodynamic conditions and can vary widely. The carbonate precipitated during inorganic carbon metabolism on coral reefs is an important part of global carbonate reservoir, which contributes 23%-26% of global CaCO3 accumulation and affects atmospheric CO2 concentration. Net organic\|to\|inorganic carbon production ratio (ROI) is developed as a criterion in reflecting the sink/source behavior of CO2 on coral reefs. When ROI is less than 0.6, the coral reef is the source of atmospheric CO2, otherwise the coral reef acts as a sink of atmospheric CO2. The recent work has established the preliminary understanding on the biogeochemical process of coral reef carbon cycle, thus the ongoing research will cover the mechanism of efficient organic carbon cycle of coral reefs, the function of coral reef organisms on carbon cycle, and the response of coral reef carbon cycle to climate change etc.