Pacific low-latitude western boundary currents region east of the Philippine coast is characterized by abundant meso-scale eddies in the subsurface layer, which play crucial roles in the intraseasonal variation of the currents and transport of subsurface waters. Based on mooring measurements and model outputs, the generation and associated kinetic energy variation of these subthermocline eddies are investigated. The results indicate that significantly high eddy kinetic energy (EKE) appears below the thermocline east of the Philippine coast between 5º-14ºN, which is caused by enhanced subthermocline eddy activities. Separated by 10ºN, the EKE in the northern and southern part displays opposite seasonal cycle, with the magnitude reaching a maximum in early spring and minimum in summer in the northern part and reaching a maximum in summer and minimum in winter in the southern part. Moreover, significant interannual cycle of the subthermocline EKE is also detected, which seems to be closely associated with ENSO events and generally lags Nino3.4 index for 14 months. Further energy and instability analysis suggest that besides the baroclinic instability reported in previous studies, barotropic instability is also essential in the generation of subthermocline eddies, especially near the Mindanao coast. The seasonal and interannual variations of EKE is dominated by the modulation of barotropic instability associated with the background currents North Equatorial Undercurrent, Mindanao Undercurrent and Halmahera Eddy.