The Taipei basin, located in northern Taiwan, is formed at the intersection of the Tanshui River valley (~30 km) and the Keelung River valley (~60 km). Summer is the dry season in northern Taiwan, but the maximum rainfall in the Taipei basin occurs during 15 June–31 August. The majority of summer rainfall in this basin is produced by afternoon thunderstorms. Thus, the water supply, air/land traffic, and pollution for this basin can be profoundly affected by interannual variations of thunderstorm days and rainfall. Because the mechanism for these interannual variations is still unknown, a systematic analysis is made of thunderstorm days and rainfall for the past two decades (1993–2013). These two variables are found to correlate opposite interannual variations of sea surface temperature anomalies over the National Oceanic and Atmospheric Administration Niño-3.4 region. Occurrence days for afternoon thunderstorms and rainfall amounts in the Taipei basin double during the cold El Niño–Southern Oscillation (ENSO) phase relative to the warm phase. During the latter phase, a stronger cold/drier monsoon southwesterly flow caused by the Pacific–Japan Oscillation weakens the thunderstorm activity in the Taipei basin through the land–sea breeze. In contrast, the opposite condition occurs during the cold ENSO phase. The water vapor flux over the East/Southeast Asian monsoon region converges more toward Taiwan to maintain rainfall over the Taipei basin during the cold ENSO phase than during the warm ENSO phase.