The skewness of subsurface temperature anomaly in the equatorial Pacific Ocean shows a significant asymmetry between the east and west. A positive temperature skewness appears in the equatorial eastern Pacific, while the temperature skewness in the western and central Pacific is primarily negative. There is also an asymmetry of the temperature skewness above and below the climatological mean thermocline in the central and western Pacific. A positive skewness appears below the thermocline, but the skewness is negative above the thermocline. The distinctive vertical asymmetry of the temperature skewness is argued to be attributed to the asymmetric temperature response to upward and downward thermocline displacement in the presence of the observed upper-ocean vertical thermal structure. Because of positive (negative) second derivative of temperature with respect to depth below (above) the thermocline, an upward and a downward shift of the thermocline with equal displacement would lead to a negative temperature skewness above the thermocline but a positive skewness below the thermocline. In the far eastern equatorial Pacific, the thermocline is close to the base of the mixed layer, the shape of the upper-ocean vertical temperature profile cannot be kept. Positive skewness appears in both below the thermocline and above the thermocline in the far eastern basin. Over the central and eastern Pacific, the anomalies of the subsurface waters tend to entrain into the surface mixed layer (by climatological mean upwelling) and then affect the SST. Hence, the positive (negative) subsurface skewness in the far eastern (central) Pacific may favor positive (negative) SST skewness, which is consistent with the observational fact that more La Nina (El Nino) occur in the central (eastern) Pacific. The present result implies a possible new paradigm for El Nino and La Nina amplitude asymmetry in the eastern Pacific.