Marine cold seeps, where subsurface methane-rich fluids discharge at seafloors, are “oases of life” that sustain highly active organic carbon (OC) and iron (Fe) cycling along the global continental margins. However, the interactions between Fe and OC and their impacts on the development and long-term carbon preservation of cold seep ecosystems remain largely unknown. Here, we analyzed the reactive Fe-bound organic carbon (Fe-OC) contents, carbon isotopic compositions, and potential sources in the upper 30 cm sediments across different development stages of cold seeps in the South China Sea. We show that Fe-OC contents in surface sediments of the early-stage seep ecosystem, formed during recent hydrate exploration activities, are ~45% higher than those in the adjacent non-seep sediments, while transiting to mature seep stage, Fe-OC contents decline by 31% alongside a 48% reduction in reactive iron (FeR) contents. Over this transition, contributions of methane-derived OC to Fe-OC decrease from 24 ± 10% to 17 ± 7%. Compared with other marine non-seep sedimentary environments, cold seep sediments maintain relatively high levels of Fe-OC with significantly elevated OC:Fe molar ratios, suggesting the distinct formation and preservation mechanisms of Fe-OC associations at cold seeps. These findings highlight the key role of Fe-OC associations in retaining methane-derived OC in the early-stage seep, while a certain fraction of Fe and marine OC associations can persist through the changing redox and geochemical conditions during cold seep development. These insights are necessary to comprehend the dynamics and inner workings of carbon cycling in marine cold seeps.