The precession plays a dominant role in driving the tropical monsoon variations. Our high resolution, millennial scale marine isotope records from ODP Site 1143 in the southern South China Sea (SCS) present the detailed history of the upper ocean structure variations over the past 1.56 Ma on glacial/interglacial timescale. The cross spectral analyses between the Earth's orbital variations and the isotopic differences reveal a high coherency between the East-Asian-monsoon-related thermocline and nutricline variations of the SCS and the precession. The variations of monsoon-related isotopic difference between species also demonstrate periodicities of 11-, 12- and 14-thousand years near semi-precession which originates in the tropics, highlighting the importance of the precession in driving the east Asian monsoon changes.