Abstract Using the specified-dynamics (SD) Whole Atmosphere Community Climate Model (SD-WACCM), the effects of the Madden–Julian oscillation (MJO) on the midwinter stratosphere and mesosphere in the Southern Hemisphere (SH) are investigated. The most significant responses of the SH polar cap temperature to the MJO are found about 30 days after MJO phase 1 (P1) and about 10 days after MJO phase 5 (P5) in both the ERA-Interim data and the SD-WACCM simulation. The 200- and 500-hPa geopotential height anomalies in the SH reveal that wave trains emanate from the Indian and Pacific Oceans when the MJO convection is enhanced in the eastern Indian Ocean and the western Pacific. As a result, the upward propagation and dissipation of planetary waves (PWs) in the middle and high latitudes of the SH stratosphere is significantly enhanced, the Brewer–Dobson (BD) circulation in the SH stratosphere strengthens, and temperatures in the SH polar stratosphere increase. Wavenumber 1 in the stratosphere is the dominant component of the PW perturbation induced by the MJO convection. In the SH mesosphere, the MJO leads to enhancement of the dissipation and breaking of gravity waves (GWs) propagating as a result of wind-filtering change in the SH extratropics and causes anomalous downwelling in the middle and high latitudes of the mesosphere. The circulation thus changes significantly, resulting in anomalous cooling in the mesosphere in response to MJO P1 and P5 at lags of 10 and 30 days, respectively.
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