Abstract Anaerobic oxidation of methane (AOM) governs methane consumption at seeps, yet δ13C‐CH4 values in the sulfate‐methane transitions are commonly lower than predicted from preferential 12C utilization by methanotrophic archaea, suggesting the influence of a different methane source. To address this isotope discrepancy, we used high‐resolution ion concentrations and carbon isotope data (CH4 and DIC) of porewaters from the Haima seep, South China Sea, to reconstruct the carbon cycle using a reaction‐transport model. Model simulations demonstrate that in situ methanogenesis cannot explain the extreme 13C depletion. Instead, the shift towards 13C‐depleted CH4 and DIC is primarily driven by isotopic equilibration during AOM, modulated by the carbon isotope fractionation factor and reverse AOM reaction flux under stable conditions. This mechanistic framework reconciles the paradoxical 13C‐depletion in CH4 by emphasizing the role of carbon isotope equilibration during AOM, offering an effective method for tracing the cryptic methane cycle in seep environments.

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