Blue holes are unique geomorphological features with steep biogeochemical gradients and distinctive microbial communities. Carbon cycling in blue holes, however, remains poorly understood. Here we describe potential mechanisms of dissolved carbon cycling in the world's deepest blue hole, the Yongle Blue Hole (YBH), which was recently discovered in the South China Sea. In the YBH, we found some of the lowest concentrations (e.g., 22 μM) and oldest ages (e.g., 6,810 years before present) of dissolved organic carbon, as well as the highest concentrations (e.g., 3,090 μM) and the oldest ages (e.g., 8,270 years before present) of dissolved inorganic carbon observed in oceanic waters. Sharp gradients of dissolved oxygen, H2S, and CH4 and changes in bacterially mediated sulfur cycling with depth indicated that sulfur‐ and/or methane‐based metabolisms are closely linked to carbon cycling in the YBH. Our results showed that the YBH is a unique and easily accessible natural laboratory for examining carbon cycling in anoxic systems, which has potential for understanding carbon dynamics in both paleo and modern oceans—particularly in the context of global change.