El Niño-Southern Oscillation (ENSO) is one of the key drivers of global climate anomaly, and its evolution during geological history is crucial for understanding the natural variability of the climate system. The Middle Miocene Climatic Optimum (MMCO, 16.9–14.7 Ma) was a period of relatively warm global climate. During this period, the contraction and closure of tropical seaways exerted profound impacts on global ocean circulation and climate. Using idealized sensitivity experiments with the FGOALS-g3 model, we artificially close the Indonesian Seaway to isolate its mechanistic influence on ENSO dynamics. Although this extreme scenario does not reflect the actual open-gateway conditions of the Miocene, it allows us to clearly identify the seaway's role in modulating tropical climate variability. The results demonstrate that the closure of the Indonesian Seaway exerts a significant impact on ENSO, increasing ENSO amplitude by 140%, an impact far exceeding that of the Panama and Tethys Seaways. Diagnostics based on the mixed-layer heat budget equation reveal that the enhancement of ENSO amplitude is primarily driven by the strengthened zonal advection feedback. The closure of the Indonesian Seaway drives the formation of an "El Niño-like" mean state in the tropical Pacific, which facilitates the eastward propagation and amplification of sea surface temperature anomalies and wind stress anomalies. These findings underscore the critical role of the Indonesian Seaway in modulating ENSO variability during the MMCO and provides mechanistic insights into the potential amplifying effect of the weakening Indonesian Throughflow on ENSO under future global warming scenarios.