In order to explore the biogeochemical process of the rare earth elements in deep sea pore water, high-precision samples were collected from the two stations of the Philippine Sea. Geochemical characteristics of the main elements, trace elements and REE are analyzed and the concentration, distribution and fractionation of the REE discussed in details. It is found that both the two stations are in an oxidizing environment. HREE and MREE are enriched around the water-sediment interface and in the shallow pore water (2.5～20 cm), while MREE and HREE enriched in the middle (25～60 cm) and lower layers of sediments. We believe that the decomposition and adsorption of organic matter and Mn oxide are the main factors for the fractionation of REE in pore water. Concentrations and fractionations of REE in pore water are found different in the East and West sides of the Kyushu Palau Ridge because of the difference in volcanic activities, mineral composition and Mn oxide in the surrounding environment. However, the pore fluid of the study area makes no contribution of REE to the ocean.