As the most prominent decadal variability in the Pacific Ocean, the Pacific Decadal Oscillation (PDO) can influence the El Niño‐Southern Oscillation‐related atmospheric and upper oceanic motions. Based on results from ocean reanalysis products and linear continuously stratified model experiments, we reveal that the PDO can further extend its interdecadal modulation effect to the equatorial intermediate currents below the thermocline. For the maximum El Niño‐related intermediate eastward transport anomaly in the western Pacific, its magnitude during the warm PDO is nearly twice as large as that during the cold PDO, and its occurrence time in the warm PDO leads that in the cold PDO by about 2 months. Such modulation is achieved through westward and downward propagation of the reflected Kelvin‐to‐Rossby waves, triggered by enhanced and eastward‐displaced anomalous westerly wind. The decisive wind forcing region for the modulation is located over the equatorial central Pacific of 5°S–5°N and 180°–140°W. Plain Language Summary: Variability of the Equatorial Intermediate Currents (EICs) below the thermocline at decadal and longer periods is rarely explored. The EICs in the western Pacific show a significant interannual response to El Niño‐Southern Oscillation at a 10‐ to 12‐month lag, with an eastward anomaly transport (Tra) during the El Niño events. This study demonstrates that the El Niño‐related eastward Tra can be further modulated by the Pacific Decadal Oscillation (PDO). First, the magnitude of maximum eastward Tra induced by El Niño in the warm PDO phase is twice as large as that in the cold PDO phase. Second, the occurrence time of the largest eastward Tra during the warm PDO peaks 2 months earlier than that during the cold PDO. We performed model experiments to explore the underlying mechanism. The above modulation is closely related to the wind forcing in the equatorial central Pacific. In the warm PDO phase, the enhanced and eastward‐displaced anomalous westerly winds can induce the Kelvin waves with an intensified amplitude and eastward shift. These eastward propagating waves are reflected into Rossby waves at the Pacific eastern boundary. The westward and downward propagation of such Rossby waves induce the larger and earlier peaked eastward Tra. Key Points: Maximum intermediate transport anomaly (Tra) induced by El Niño in warm PDO doubles and peaks 2‐month earlier than that in cold PDO Tra difference is attributed to magnitude change and longitude shift of anomalous westerly winds in the equatorial central PacificWinds induce Tra through generating reflected Kelvin‐to‐Rossby waves with an enhanced amplitude and westward displacement in warm PDO [ABSTRACT FROM AUTHOR]