Since the early Cenozoic, the West Philippine Basin (WPB) and the whole Philippine Sea Plate (PSP) has undergone a complex geological evolution. In this study, we presented K-Ar ages, in situ trace element, and major element compositions of minerals of basalts collected from the Benham Rise and the Central Basin Fault (CBF) in the WPB, to constrain their magmatic process and regional geological evolution. Olivine phenocrysts and microlites in the alkali basalts (20.9 Ma) from the Benham Rise have forsterite (Fo) contents of 56.90%–76.10% and 53.13%-66.41%, respectively. The clinopyroxenes in the tholeiites (29.1 Ma) from the CBF is predominantly diopside and augite, and it is depleted in light rare earth elements (LREEs) (LaN/YbN=0.13–3.40) and large-ion lithophile elements (LILEs). The plagioclases in the basalts from both of the Benham Rise and the CBF are predominantly labradorite and andesine, with a minor amount of bytownite, and it is enriched in LREEs, Ba, Sr, and Pb and exhibits strong positive Eu anomalies. However, there exist obvious differences in plagioclase compositions between these two tectonic sites. The source lithology of the Benham Rise basaltic rocks could be garnet pyroxenite, and yet that of the CBF could be spinel-lherzolite. The calculated mantle potential temperature beneath the Benham Rise is 1439°C–1473°C, which is significantly higher than that beneath the CBF (1345°C–1381°C), suggesting there existed thermal anomaly beneath the Rise during basaltic magmatism. This study also calculated the temperature and pressure of the clinopyroxenes and plagioclases, which have been used to indicate magmatic processes. Finally, we suggest that the Benham Rise basaltic rocks may be related to a mantle plume (e.g., the Oki-Daito mantle plume), and the CBF was once located in a back-arc spreading center behind an active subduction zone. The extinction of the Oki-Daito mantle plume activity might be at about 20.9 Ma, and cessation of the back-arc spreading of WPB was at about 29.1 Ma or younger.