Interannual variation of subthermocline eddy kinetic energy (EKE) east of the Philippines is investigated based on mooring measurements during 2015-2019 and ocean state estimates during 1995-2017 from the Oceanic General Circulation Model for the Earth Simulator (OFES). Prominent interannual variation of EKE is detected below the thermocline east of the Philippine coast, which is closely related to the El Niño and Southern Oscillation (ENSO) events and generally lags the Nino3.4 index by 14 months. Further energy diagnostic analysis indicates that the interannual variation of subthermocline EKE is controlled by both baroclinic and barotropic instability of the background flows and dominated by the barotropic instability especially. Barotropic instability in the southern part of the Philippine coast is associated with the subsurface component of the quasi-permanent anticyclonic eddy Halmahera Eddy (HE), while that in the northern part is closely related to the Mindanao Undercurrent (MUC). Both HE and MUC are modulated by the ENSO events. When El Niño occurs, negative sea surface height anomalies appear near the dateline and propagate westward in the form of the first mode baroclinic Rossby wave, exerting delayed impacts upon the western boundary currents east of the Philippine coast and further modulating the interannual variation of subthermocline EKE. Moreover, the barotropic energy conversion rate and its corresponding subthermocline EKE at lower latitudes responds relatively faster to ENSO due to the higher Rossby wave phase speed there.