This paper explores the Madden–Julian Oscillation (MJO) modulation of tropical cyclone (TC; hereafter, MJO-TC) genesis over the South China Sea (SCS) and Western North Pacific (WNP) under different El Niño-Southern Oscillation (ENSO) conditions. Analyses used Joint Typhoon Warning Center (JTWC) best-track data, the Real-Time Multivariate MJO (RMM) index, and European Center for Medium-Range Weather Forecasts (ECMWF) Interim (ERA-Interim) reanalysis data. The results showed that the MJO has significant modulation on both the SCS and WNP TC genesis in neutral years, with more (fewer) TCs forming during the active (inactive) MJO phases. However, during the El Niño and La Niña years, the MJO-TC genesis modulation over the two regions differs from each other. Over the SCS, the MJO modulation of TC genesis is stronger in the La Niña years, while it becomes weaker in the El Niño years. Over the WNP, the MJO has a stronger influence on TC genesis in the El Niño years compared to that in the La Niña years. Related Genesis Potential Index (GPI) analysis suggests that midlevel moisture is the primary factor and vorticity is the secondary factor, for the MJO-TC genesis modulation over the SCS in the La Niña years. Over the WNP, midlevel moisture is the dominant factor for the MJO-TC genesis modulation during the El Niño years. These results can be explained by increased water vapor transport from the Bay of Bengal, associated with enhanced westerly wind anomalies, during the active phases relative to the inactive MJO phases; these conditions prevail over the SCS during the La Niña years, and over the WNP during the El Niño years.