This study examines the interannual variation of the Convective Afternoon Rainfall (CAR) activity (including frequency and intensity) in Taiwan during the summers (JJA) of 1961–2012 with a focus on identifying its relationship with the changes in sea surface temperature anomalies over the Niño3.4 region [SSTA(Niño3.4)] and the underlying physical mechanisms. Our analyses show that during the colder (warmer) phase of SSTA(Niño3.4), the subtropical high system over the region east of Taiwan is enhanced (weakened), the local surface wind convergence is enhanced (weakened), and the local thermal instability is enhanced (weakened), which facilitates (suppresses) the formation of CAR in Taiwan. This consistent negative relationship between the interannual variation of CAR frequency in Taiwan and SSTA(Niño3.4) occurs throughout 1961–2012. In contrast, the relationship between the interannual variation of CAR intensity in Taiwan and SSTA(Niño3.4) changed from positively correlated to negatively correlated in the late 1980s. This change is attributed to the change in the moisture supply for maintaining the CAR intensity in Taiwan from an increase (decrease) in the warmer (colder) phase of SSTA(Niño3.4) before the mid-1980s to the opposite after the late 1980s. These findings highlight how the rainfall characteristics in East Asia may change in response to changes in SSTA(Niño3.4).