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Abstract El Niño-Southern Oscillation (ENSO) exhibits diverse characteristics in spatial pattern, peak intensity, and temporal evolution. Here we develop a three-region multiscale stochastic model to show that the observed ENSO complexity can be explained by combining intraseasonal, interannual, and decadal processes. The model starts with a deterministic three-region system for the interannual variabilities. Then two stochastic processes of the intraseasonal and decadal variation are incorporated. The model can reproduce not only the general properties of the observed ENSO events, but also the complexity in patterns (e.g., Central Pacific vs. Eastern Pacific events), intensity (e.g., 10–20 year reoccurrence of extreme El Niños), and temporal evolution (e.g., more multi-year La Niñas than multi-year El Niños). While conventional conceptual models were typically used to understand the dynamics behind the common properties of ENSO, this model offers a powerful tool to understand and predict ENSO complexity that challenges our understanding of the twenty-first century ENSO.