Tian et al. (2007) found that the MJO-related total column ozone (O<sub>3</sub>) anomalies of 10 DU (peak-to-trough) are mainly evident over the subtropics and dynamically driven by the vertical movement of the subtropical tropopause layer. It was then hypothesized that the subtropical total column O<sub>3</sub> anomalies are primarily associated with the O<sub>3</sub> variability in the stratosphere rather the troposphere. In this paper, we investigate the vertical structure of MJO-related subtropical O<sub>3</sub> variations using the vertical O<sub>3</sub> profiles from the Aura Microwave Limb Sounder (MLS) and Tropospheric Emission Spectrometer (TES), as well as in-situ measurements by the Southern Hemisphere Additional Ozonesondes (SHADOZ) project. Our analysis indicates that the subtropical O<sub>3</sub> anomalies maximize approximately in the lower stratosphere (60–100 hPa). Furthermore, the spatial-temporal patterns of the subtropical O<sub>3</sub> anomalies in the lower stratosphere are very similar to that of the total column. In particular, they are both dynamically driven by the vertical movement of subtropical tropopause. The subtropical partial O<sub>3</sub> column anomalies between 30–200 hPa accounts for more than 50 % of the total O<sub>3</sub> column anomalies. TES measurements show that at most 27 % of the total O<sub>3</sub> column anomalies are contributed by the tropospheric components. This indicates that the subtropical total column O<sub>3</sub> anomalies are mostly from the O<sub>3</sub> anomalies in the lower stratosphere, which supports the hypothesis of Tian et al. (2007). The strong connection between the intraseasonal subtropical stratospheric O<sub>3</sub> variations and the MJO implies that the stratospheric O<sub>3</sub> variations may be predictable with similar lead times over the subtropics. Future work could involve a similar study or an O<sub>3</sub> budget analysis using a sophisticated chemical transport model in the near-equatorial regions where the observed MJO signals of total column O<sub>3</sub> are weak.