Vertical mixing is an important factor in determining the temperature, sharpness and depth of the equatorial Pacific thermocline, which are critical to the development of El Ninõ and Southern Oscillation (ENSO). Yet, properties, dynamical causes and large-scale impacts of vertical mixing in the thermocline are much less understood than that nearer the surface. Here, based on Argo float and the Tropical Ocean and Atmosphere (TAO) mooring measurements, we identify a large number of thermocline mixing events occurring down to the lower half of the thermocline and the lower flank of the Equatorial Undercurrent (EUC), in particular in summer to winter. The deep-reaching mixing events occur more often and much deeper during periods with tropical instability waves (TIWs) than those without and under La Niña than under El Niño conditions. We demonstrate that the mixing events are caused by lower Richardson numbers resulting from shear of both TIWs and the EUC.