The response of tropical cyclone (TC) activity to the El Niño-Southern Oscillation (ENSO) and coherent sea surface temperate (SST) anomaly in the Indian Ocean (IO) is investigated with a particular focus on the decaying phase of El Niño. The TC anomalies are obtained from the database for Policy Decision making for Future climate change (d4PDF). This dataset is based on 100-member ensemble simulations for the period of 1951-2010 by use of the state-of-the-art atmospheric general circulation model (AGCM) forced with observed SST as well as the historical radiative forcing. AGCM utilized in the d4PDF is the Meteorological Research Institute Atmospheric General Circulation Model with about 60km horizontal resolution. Our analysis reveals a prolonged decrease in TC frequency over the tropical western Pacific during the post El Niño years until the boreal fall. Dominance of anomalous anticyclone (AAC) over the western Pacific induced by the delayed warming in the tropical Indian Ocean is the main factor for the suppressed TC activity rather than the local SST change. In contrast, the TC number over the South China Sea tends to increase during the post-El Niño fall (September to November). The physical reason can be ascribed to the weakening of AAC associated with the termination of IO warming. Thus we demonstrate that the effect of the IO warming should be taken into account when the ENSO is considered as an environmental factor for predicting TC activity.