Abstract Convection anomalies in the eastern and western Maritime Continent (MC) during boreal autumn exhibit distinct characteristics and climatic effects, but their impacts on South China Sea (SCS) tropical cyclones (TCs) remain unclear. Here we reveal that the eastern MC convection mode, although it explains less convection variance, exerts strong influences on autumn SCS TCs by positioning anticyclonic anomalies directly over the SCS to suppress TC activity. In contrast, the western MC convection shifts the anticyclonic center toward the Indian Ocean and induces little impact on SCS TCs. Furthermore, the eastern MC convection is linked to Phase 2 + 3 and Phase 5 of intraseasonal Madden‐Julian Oscillation, which are phases that strongly impact SCS TCs. By examining both seasonal and intraseasonal timescales, this study highlights the multi‐timescale influences of regional MC convection on SCS TC activity and provides new insights into the climatic effects of shifting MC convection.