In this paper, determinations of phosphorus forms, methane and sulfate and so on were implemented in the typical pockmark area of north Yellow Sea to explore the controlling mechanism of phosphorus transformation and burial under this unique environment and its effect of phosphorus release from sediment-water system on regional phosphorus cycle. The results showed that Det-P(>50%) was the dominant P form in the sediments, followed by Org-P, Fe-P and Auth-P. Exch-P was the minor phase of Tot-P. The diffusive fluxes of dissolved reactive phosphorus (DRP) at B9 and B11 stations were 2.84μmol/(cm²·a) and 1.03μmol/(cm²·a), and their contributions to surface water P loadings were 19.6% and 3.03%, respectively. Observed burial and transformation of phosphorus in and out the pockmark were different; the leakage of groundwater in the study area was the reason for both the high deposition rate and release flux of phosphorus. The preservation of phosphorus in the sediments of the pockmark area in the north Yellow Sea was also related to the escape of shallow methane, which could possibly enhance the formation of pyrite in cores. The higher DRP flux in the sediment-water interface would yield some ecological environment problems like regional eutrophication, which would have far-reaching ecological influence and should be thus worthy of more attention.