Abstract The mean vertical advection of anomalous vertical temperature gradient is considered the dominant generation mechanism of positive sea surface temperature (SST) anomalies associated with the canonical El Niño. However, most past studies had a residual term in their heat budget analysis and/or did not quantify the role of vertical mixing even though active vertical turbulent mixing in the upper ocean is observed in the eastern equatorial Pacific. To quantitatively assess the importance of vertical mixing, a mixed layer heat budget analysis is performed using a hindcast simulation forced by daily mean atmospheric reanalysis data. It is found that when the mixed layer depth is defined as the depth at which potential density increases by 0.125 kg m−3 from the sea surface, the development of positive SST anomalies is predominantly governed by reductions in the cooling by vertical mixing, and their magnitude is much larger than those by vertical advection. The anomalous warming by vertical mixing may be partly explained by an anomalous deepening of the thermocline that leads to a decrease in the vertical temperature gradient, giving rise to suppression of the climatological cooling by vertical mixing. Also, an anomalously thick mixed layer reduces sensitivity to cooling by the mean vertical mixing and contributes to the anomalous SST warming. On the other hand, the dominant negative feedbacks are attributed to both anomalous surface heat loss and anomalous deepening of the mixed layer that weakens warming by the mean surface heat flux.