Extreme storm surges severely affect densely populated coasts and offshore islands across the Indo-Pacific. These extremes are strongly modulated by major climate variability modes, including the El Niño–Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), Pacific Decadal Oscillation (PDO), Pacific–North American (PNA), Northern Annular Mode (NAM), and Southern Annular Mode (SAM) patterns. This study examines their seasonal influence on extreme storm surges during 1979–2018 using GTSM/ERA5 reanalysis data and Generalized Extreme Value (GEV) analysis based on block maxima. ENSO|PDO intensifies extreme surges over the western and eastern Pacific throughout the year, with pronounced enhancement during boreal summer (JJA), while suppressing surge intensity along the Indonesian coast. The IOD exerts significant control over the northern Pacific and southern Australia in boreal spring (MAM), and across the Indian Ocean and Pacific sectors in JJA. PDO|ENSO intensifies storm surge over the North and western Pacific during SON. The PNA notably affects the Gulf of Thailand, Gulf of Carpentaria, and eastern Pacific during boreal winter (DJF), with impacts shifting toward the western North Pacific in JJA. In-phase ENSO–IOD and ENSO–PDO events produce amplified and statistically significant surge extremes, particularly during DJF and JJA.