El Niño’s intensity change under anthropogenic warming is of great importance to society, yet current climate models’ projections remain largely uncertain. The current classification of El Niño does not distinguish the strong from the moderate El Niño events, making it difficult to project future change of El Niño’s intensity. Here we classify 33 El Niño events from 1901 to 2017 by cluster analysis of the onset and amplification processes, and the resultant 4 types of El Niño distinguish the strong from the moderate events and the onset from successive events. The 3 categories of El Niño onset exhibit distinct development mechanisms. We find El Niño onset regime has changed from eastern Pacific origin to western Pacific origin with more frequent occurrence of extreme events since the 1970s. This regime change is hypothesized to arise from a background warming in the western Pacific and the associated increased zonal and vertical sea-surface temperature (SST) gradients in the equatorial central Pacific, which reveals a controlling factor that could lead to increased extreme El Niño events in the future. The Coupled Model Intercomparison Project phase 5 (CMIP5) models’ projections demonstrate that both the frequency and intensity of the strong El Niño events will increase significantly if the projected central Pacific zonal SST gradients become enhanced. If the currently observed background changes continue under future anthropogenic forcing, more frequent strong El Niño events are anticipated. The models’ uncertainty in the projected equatorial zonal SST gradients, however, remains a major roadblock for faithful prediction of El Niño’s future changes.