We deployed 27 ocean-bottom seismometers (OBSs) and five Macquarie Island stations between 2020 and 2021 along the Australian-Pacific plate boundary in the Macquarie Ridge Complex (MRC) of the Southern Ocean. From the waveforms recorded on successfully recovered OBSs and the island stations, including permanent station MCQ, we generated a 3-D S-wave velocity model for the crust and uppermost mantle using full-waveform ambient noise tomography. Distinct surface waves are identified via inter-station cross-correlation of the vertical components. The new S-wave velocity model reveals a pronounced increase in velocity across expected crustal and uppermost mantle depths. Relatively high S-wave velocities (>3.8 km/s at 7 km below sea level) are consistent with the presence of upper mantle rocks at relatively shallow depths spread out along the ridge. Overall, our findings provide initial insights on the sub-surface structure of the MRC, a complex tectonic setting of potential subduction initiation.