By decomposing the variations of daily mean variables into synoptic, intraseasonal, and low-frequency components, the present study compares seasonal mean latent heat flux (LHF) anomalies related to the three components over the tropical Indo-Pacific region during El Niño and La Niña years. It is found that the high-frequency (intraseasonal and synoptic) LHF has an important contribution to total seasonal mean LHF anomalies over the tropical eastern Indo-western Pacific region. Large seasonal mean LHF anomalies related to high-frequency wind variations are identified in weak low-frequency seasonal mean wind regions where high-frequency LHF may accumulate over a season as it increases in both westerly and easterly phases of high-frequency wind variations. In those regions, the LHF anomalies related to high-frequency wind variations cancel part of the low-frequency LHF anomalies, reducing total seasonal mean LHF anomalies. As El Niño-Southern Oscillation (ENSO)-induced lower-level wind anomaly region moves with the stage of ENSO, large seasonal mean LHF anomalies related to high-frequency wind variations displace with the season. The intensity of high-frequency wind fluctuations is also a factor influencing the seasonal mean LHF related to high-frequency wind variations. Thus, the ENSO affects the high-frequency LHF variations through modulating both the location of weak low-frequency wind region and intensity of high-frequency wind fluctuations.