The interannual fluctuations of the equatorial thermocline are usually associated with El Niño activity, but the linkage between the thermocline modes and El Niño is still under debate. In the present study, a mode function decomposition method is applied to the equatorial Pacific thermocline, and the results show that the first two dominant modes (M1 and M2) identify two distinct characteristics of the equatorial Pacific thermocline. The M1 reflects a basinwide zonally tilted thermocline related to the eastern Pacific (EP) El Niño, with shoaling (deepening) in the western (eastern) equatorial Pacific. The M2 represents the central Pacific (CP) El Niño, characterized by a V-shaped equatorial Pacific thermocline (i.e., deep in the central equatorial Pacific and shallow on both the western and eastern boundaries). Furthermore, both modes are stable and significant on the interannual time scale, and manifest as the major feature of the thermocline fluctuations associated with the two types of El Niño events. As good proxies of EP and CP El Niño events, thermocline-based indices clearly reveal the inherent characteristics of subsurface ocean responses during the evolution of El Niño events, which are characterized by the remarkable zonal eastward propagation of equatorial subsurface ocean temperature anomalies, particularly during the CP El Niño. Further analysis of the mixed layer heat budget suggests that the air–sea interactions determine the establishment and development stages of the CP El Niño, while the thermocline feedback is vital for its further development. These results highlight the key influence of equatorial Pacific thermocline fluctuations in conjunction with the air–sea interactions, on the CP El Niño.