The low-frequency variability of the North Equatorial Current (NEC) bifurcation during 1958 to 2001 was investigated with the Simple Ocean Data Assimilation (SODA) 2.0.2 dataset. In agreement with recent observations, the NEC bifurcation latitude (NBL) shifted northward as depth increases, from about 12.7°N near the surface to about 17.1°N at depths around 500 m for the annual average. This study reveals that the interannual variations of NBL, with five years period, mainly focused on the upper 500 m with amplitude increasing as depth increased. The NBL shifted southward in the past 40 years, which was more significant in the subsurface at more than −0.02°/a. The NBL manifests itself in the transports of NMK (NEC-Mindanao Current (MC)-Kuroshio) system in strong relationship with MC (0.7) and Kuroshio (−0.7). The EOF analysis of meridional velocity off the Philippine coast shows that the first mode, explaining 62% of variance and 5 years period, was highly correlated with the southward shift of NBL with coefficient at about 0.75. The southward shift of NBL consists with the weakening of MC and strengthening of Kuroshio, which exhibited linear trends at −0.24Sv/a and 0.11Sv/a. Both interannual variation and trend of NBL were closely related to the variation of NMK system.