The evaporation duct, formed above the ocean surface by sharp vertical gradients of humidity, would significantly influence electromagnetic wave propagation. It is a quasi-permanent feature over the sea, and its strength is quantified by the evaporation duct height (EDH). While previous studies have focused on how local factors influence evaporation ducts, the impact of El Niño–Southern Oscillation (ENSO) on EDH in the South China Sea (SCS) remains undocumented. Using correlation analysis, empirical orthogonal function (EOF) decomposition, and wavelet transform, this study shows that evaporation is the dominant environmental factor controlling EDH variability across seasonal and inter-annual timescales in the SCS, while wind speed and relative humidity play secondary roles with contrasting effects between the northern and southern regions. ENSO drives the inter-annual variability of EDH by modulating evaporation. During El Niño events, anomalous anticyclonic circulations near the Philippine Sea, which weaken (strengthen) the evaporation in the northern (southern) SCS, alter EDH and contribute to the formation of the meridional dipole structure, particularly within the 2-to-6-year ENSO band. These results provide new insights into the mechanisms controlling EDH in the SCS and highlight the critical role of ENSO in shaping its spatial distribution.