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Extreme El Niño events affect the number of intense tropical cyclones (ITCs) over the western North Pacific (WNP). In 1997 and 2015, both extreme El Niño years, ITC numbers were above normal in the WNP. In order to clarify how, and to what extent, sea surface temperature anomaly (SSTA) distributions control the ITCs genesis, the authors conducted 50‐member ensemble simulations using a high‐resolution global nonhydrostatic model that explicitly simulates ITCs. The ensemble simulations showed a clear relationship between the number of ITCs and their genesis locations in the WNP. However, the authors found that the simulated numbers of ITCs in the WNP were also closely related to the strength of the monsoon trough, which varies under given SSTA conditions. This indicates that reliable seasonal forecasting of ITCs depends on our ability to accurately reproduce the monsoon trough, whose strength is modulated mainly by internal atmospheric variability but also by SSTA. Plain Language Summary: Tropical cyclone has a potential to cause great loss of life and damage to infrastructure. Accurate prediction of tropical cyclone activity can reduce these loss and damage. However, deterministic prediction of tropical cyclone is difficult. Development of tropical cyclones is affected by sea surface temperature and its geographical distribution (e.g., El Niño). To evaluate variability of intense tropical cyclone activity, we conducted 50‐member simulations under an identical sea surface temperature condition. Although the simulation shows the number of intense tropical cyclones differs among members despite the identical sea surface condition, the number is strongly related to the atmospheric response to the sea surface temperature. Over the western North Pacific, the monsoon trough is strongly contributing to tropical cyclone genesis and its genesis location. The simulated number was correlated with the strength of westerly wind associated with the monsoon trough. The response of the monsoon trough to the sea surface temperature itself also shows variations. However, the response was partially predictable by the sea surface temperature. This study shows that the reproducibility of the monsoon trough plays a key role in reliable seasonal forecasting of intense tropical cyclones. Key Points: Fifty‐member ensemble simulations of 1997 and 2015 assessed the impact of El Niño on intense tropical cyclones in the western North PacificThe intense tropical cyclone numbers substantially varied among ensemble members, despite their use of identical sea surface temperatureThe strength of westerly wind associated with the monsoon trough played a key role in predicting the number of intense tropical cyclones [ABSTRACT FROM AUTHOR]