Phosphorus (P) is an important nutrient for biological communities in cold seeps. However, our knowledge on the source, species, and cycling of P in cold seep environments is limited. In this study, the concentration, species, and micro to nanometer scale distribution of P in seep carbonates were examined at three deep-sea cold seeps in the South China Sea and East China Sea. The Ca-P accounts for the largest proportion of P—followed by detrital-P, Fe-P, organic-P, and exchangeable-P. The distribution patterns of Ca-P, detrital-P, and organic-P in the seep carbonates differ from one another, as shown by elemental mapping with NanoSIMS and scanning electron microscopy. The covariation of P with Ca and C reveals that Ca-P co-precipitates with Ca-carbonate, which is linked to the process of sulfate-driven anaerobic oxidation of methane. Organic-P is also observed within biofilm-like organic carbon aggregates, revealing the microbial enrichment of P by fluids in the process of anaerobic oxidation of methane. P with a granulated morphology was identified as detrital-P derived from deep sediments. Most importantly, it is evident that Ca-P is positively correlated to the Fe content in all the seep carbonates. This indicates the likelihood that the dissolved P in cold-seep fluids is released primarily from Fe oxides through Fe-driven anaerobic oxidation of methane in deep sediments. These processes associated with different species of P may have significant implications for P geochemical cycling and anaerobic oxidation of methane impelled by Fe and sulfate reduction in cold seep environments.