Seep carbonates are commonly used to study environmental conditions based on trace element patterns. However, the relationship between methane flux and trace element enrichments is not well understood. Tubular seep carbonates, which are interpreted as former fluid conduits, offer an opportunity to investigate how trace element distributions in these structures respond to changes in methane flux. Here, we examined the distribution of trace elements in three tubular seep carbonates collected from Jiulong Methane Reef in the northern South China Sea. The carbonates exhibit low δ13C values (−57.0‰ to −40.4‰ V-PDB). All tubes show a gradual increasing trend in the carbonate contents and a decreasing trend in δ13C values from the outer to the inner portions, indicating an overall increase in methane flux over time. The two tubular carbonates with lower carbon isotopic values likely precipitated in a more reducing environment, as evidenced by relatively higher enrichment factors of Molybdenum (MoEF) and higher Molybdenum/Uranium (Mo/U) ratios. The MoEF values show an increasing trend for the outer to the inner portions for the two samples with lower δ13C values, while the UEF values show an increasing trend for the two samples with higher δ13C values. This suggests that the enrichments of Mo and U are influenced by methane flux, which regulates the redox conditions and the rate of elements supplied from seawater. Only Arsenic (As) and antimony (Sb) show identifiable enrichment among the other trace elements, which is unrelated to methane dynamics. This study provides insights into the behavior of redox-sensitive trace elements under changing methane flux, laying a groundwork for using trace element enrichments to reconstruct paleoenvironmental information, particularly in dynamic environments.