Abstract: To reveal the controlling factors of clay minerals input in the Western Pacific Warm Pool since the Late Pleistocene, we analyzed the composition, source, and mass accumulation rates (MARs) of clay minerals in the sediment from Core Ph05-5 recovered from the Benham Rise in the Western Philippine Sea. The results indicate that the clay minerals in the core sediment are mainly composed of illite (13%) and smectite (8%), followed by chlorite (6%) and kaolinite (2%). Over the last 220 ka, illite and chlorite are derived mainly from the Asian continent, and smectite is mainly authigenic Fe-smectite in volcanic origin from islands around the Philippine Sea after erosion by seawater at the seabed, and smectite formed by weathering of volcanic material from islands around the West Philippine Sea. The MARs of illite and chlorite displayed significant high value during the glacial period and low value during the interglacial period, which is consistent with the total MARs of eolian dust of Core Ph05-5, MARs of Asian dust and North Pacific dust over the last 220 ka. The decrease/enhancement of solar radiation during the glacial/interglacial period, as well as the strengthening/weakening of arid in Asian continent are the main controlling factors for the increase/decrease in the input of clay minerals, such as illite from Asian continent into the Philippine Sea. The MARs of smectite in Core Ph05-5 also exhibits high value during the glacial period and low value during interglacial period, which is consistent with the total MARs of the volcanic material in Core Ph05-5. The changes of smectite in the orbital scale are mainly controlled by global sea level change and precipitation influenced by tropical ENSO processes. The low sea level during the glacial period resulted in the strengthened mixing effect between the Philippine Island and seawater, and led to an increase of smectite input in the Philippine Sea. In addition, during the glacial period, La Niña-like process was stronger in the tropical Pacific, resulting in an increase in rainfall and increased volcanic materials (smectite) input into the Philippine Sea. On the contrary, during interglacial period, the strengthened El Niño-like process resulted in the drought in the Philippine islands, and the decreased volcanic materials (smectite) input in the Philippine Sea.