Abstract: During the formation of seep carbonates, variations in fluid seepage affect the biogeochemical processes that drive the cycling of various elements, such as carbon and sulfur. However, such an influence on iron (Fe) and phosphorus (P) cycling and related biogeochemical processes remains unclear. In this study, mineral compositions, carbon and sulfur geochemistry, Fe and P component were investigated on a cross section of a chimney-like seep carbonate sample collected from the Dongsha area of the South China Sea. Results reveal that the anaerobic oxidation of biogenic methane led to the formation of the extremely ¹³C-depleted authigenic carbonate rocks (δ¹³C_VPDB＜−55.5‰), and the addition of enriched ¹⁸O fluids from the dissociation of gas hydrates results in abnormally high oxygen isotope composition (5.5‰–5.8‰) observed in the chimney carbonates. Combined with the dominant minerals with calcite in the outer layer of the chimney carbonates and aragonite in the inner layer, we inferred that the carbonates in the inner layer were formed at the later stage under stronger methane seepage condition. The most significant P-bearing mineral in the samples is authigenic phosphate (P_Auth), and the highest content is in the inner layer of the chimney carbonates. Compared with the outer chimney sample, the inner layer has lower Fe oxide content, but higher Fe-bound P (P_Fe) content, indicating the formation of vivianite. Therefore, we believe that under a stronger seepage condition during the formation of seep carbonates, an enhanced intensity of methane seepage can affect the abundance of P_Auth and P_Fe, which may favor the formation of vivianite and authigenic phosphates, thereby influencing Fe and P cycling in cold-seep environments.