Abstract This study demonstrates that during the passage of the MJO through the Maritime Continent in the boreal winter, the corresponding deep convection and near-surface wind anomalies tend to skirt around mountainous islands. Flow bifurcation around elongated mountainous islands, such as New Guinea, is clearly seen. Topographic blocking generates distinctive vorticity and convergence distributions in this specific domain. Mountain-wave-like structures are also observed throughout the Maritime Continent, with a clear spatial relationship with the high terrains in Sumatra, Sulawesi, and New Guinea. The existence of topography seems to create extra lifting and sinking within the large-scale circulation and thus the convective system exhibits quasi-stationary features near the major topography during the MJO passage through the Maritime Continent. It is suggested that resolving the detailed topographic effects may play a key role in simulating realistic characteristics of the MJO in the Maritime Continent.