The recent decades have experienced changes in the characteristics of the El Niño phenomenon, with in particular an increased occurrence of so-called Modoki or Central Pacific El Niños. Here the 2002/2003 El Niño, characterized as a Central Pacific El Niño, is studied from an Ocean General Circulation Model simulation. The focus is on the sequence of equatorial waves and their impact on zonal and vertical advection. The wave amplitude according to the most energetic baroclinic modes are first estimated, which allows inferring the sequence of the intraseasonal equatorial Kelvin (IKW) and Rossby (IRW) waves. It is shown that energetic downwelling IKWs, forced in the western-central Pacific, crossed the equatorial Pacific. Reflections of IKWs into IRWs onto the zonally varying thermocline and eastern boundary are also observed. A simplified heat budget of the surface layer is then carried out to infer the dominant processes at work during the evolution of this event focusing on the wave-induced advection terms. The results indicate that the warming phase (April–November 2002) is mainly controlled by zonal advection of mean temperature (accounted for by IKWs and locally wind-driven current) and by vertical advection in the eastern Pacific. The cooling phase (December 2002 to April 2003) is dominated by a reduction in solar radiation and the IRW-induced zonal advection of mean temperature respectively in the central and eastern equatorial Pacific. The recharge-discharge process is also showed to be at work with the recharge (discharge) process operating mainly through the second (first) baroclinic mode.