The vast tropical Pacific is home to the majority of tropical cyclones (TCs) which threaten the rim countries every year. The TC genesis is nourished by warm sea surface temperatures (SSTs). During El Niño, the western Pacific warm pool extends eastward. However, the number of TCs does not increase significantly with the expanding warm pool and it remains comparable between El Niño and La Niña. Here, we show that the subsurface heat content change counteracts the favorable SSTs in the tropical central-north Pacific. Due to the anomalous positive wind stress curl, the 26 °C isotherm shoals during El Niño over this region and the heat content diminishes in the tropical central-north Pacific, even though warm SST anomalies prevail. This negative correlation between SST and 26 °C isotherm depth anomalies is opposite to the positive correlation in the tropical eastern and western Pacific. This is critical because quantifying the dynamics of the subsurface ocean provides insight into TC genesis. The trend in TC genesis continues to be debated. Future projections must account for the net effect of the surface-subsurface dynamics on TCs, especially given the expected El Niño-like pattern over the tropical Pacific under global warming.