Calcium carbonate ($CaCO_3$) content was measured from 3 box core (BC060301, BC060303, BC070301) sediments, in addition to pilot core (PC313) sediments, from deep waters within the Western Pacific Ocean. At the two collection sites (BC060301, PC313) located close to the equator, downcore variation exhibited low $CaCO_3$ content during the interglacial period and high $CaCO_3$ content during the glacial period. Variation of coarse fraction (>$63;{mu}m$) content also followed changes in $CaCO_3$ content, indicating that dissolution effect of bottom water decreased during the glacial period. Such variation pattern is typical of the Pacific Ocean. However, downcore variation at the two collection sites (BC060303, BC070301) in the Philippine Sea contrasted the trend of the previous two cores (i.e., high $CaCO_3$ content during the interglacial period and low during the glacial period). This pattern is typical of the Atlantic Ocean. Such results may be attributed to the increasing dilution effect, initiated possibly by the increased transportation of terrigenous materials from nearby continent and archipelago during the glacial period when sea level was low. Alternatively, it is possible that the non-carbonate biogenic particles may have been responsible for dilution. Because of these uncertainties, the record of $CaCO_3$ variation in the deep Western Pacific Ocean is not regionally consistent.