Decadal modulation of El Niño/Southern Oscillation (ENSO) amplitude is reproduced by a long‐term simulation with an atmosphere‐ocean general circulation model. A frequency of the modulation is in phase with Pacific decadal variability (PDV). A detailed analysis of the budget of sea surface temperature (SST) shows that effect of a change in anomalous zonal advection of mean temperature correlated to ENSO development has a dominant role in low‐frequency modulation of ENSO. That is because an equatorial zonal SST gradient changes periodically in the PDV cycle as a change in the background mean state for ENSO. Such characteristics are consistent with an observed climate shift and changes in ENSO characteristics that occurred in mid‐1970s.