The tropical Indo-Pacific Ocean plays a central role in regulating global climate, yet the subsurface response of the South Indian Ocean (SIO) to large-scale climate variability remains poorly constrained. Here we use Argo observations to show that, despite rapid surface warming, the SIO subsurface has experienced significant basin-scale cooling and freshening over the Argo era (2004–2024). These trends exhibit marked zonal contrasts between the eastern and western SIO, suggesting distinct mechanisms and propagation pathways. Through a spice/heave decomposition, we demonstrate that long-term cooling and freshening in both regions are primarily driven by spice (along-isopycnal) changes, while heave (vertical isopycnal displacement) dominates smaller-scale variability linked to tropical climate modes, including ENSO and the Indian Ocean Dipole (IOD). Freshening accounts for much of the along-isopycnal cooling, underscoring the dominant role of salinity in shaping subsurface thermal trends across the subtropical Indo-Pacific. Both eastern and western SIO anomalies originate from multiple source regions, reflecting complex interactions between water mass formation and tropical–extratropical climate variability. We discuss the mechanisms underlying spice- and heave-driven changes and propose potential pathways for anomaly propagation across the SIO. Our findings highlight the need to better constrain the multiple sources and pathways of subsurface changes and their connections to tropical climate modes.