Oceans absorb more than 90% of the excess heat generated by anthropogenic climate change, yet the mechanisms governing how this heat is stored in contrasting basin types remain poorly resolved. This study analyzes multi-decadal changes (1955–2022) in sea surface temperature (SST) and depth-resolved upper-ocean heat content (OHC) [derived from vertically integrated subsurface temperature profiles] in two adjacent but dynamically distinct systems: the semi-enclosed Persian Gulf and the open, Indian Ocean–connected Sea of Oman. Using subsurface temperature data from the World Ocean Atlas 2023 (WOA23) and SST data from NOAA/NCEI, we analyze vertical thermal structures across seven decadal periods. Although both basins exhibit significant long-term increases in heat content, their vertical accumulation pathways differ fundamentally in their vertical distribution. In the shallow, stratified Persian Gulf, warming is strongly amplified at the surface and largely confined to the upper 50 m (trend of +0.052°C yr⁻¹ in the 0–25 m layer), indicating limited vertical mixing and restricted downward heat transfer due to intense evaporation, high salinity, and strong density stratification. In contrast, the open Sea of Oman displays vertically coherent warming extending to at least 100 m, with positive temperature and OHC trends throughout the water column, consistent with enhanced mixing and oceanic exchange with the Indian Ocean. Decadal-scale coupling between SST and subsurface OHC further reveals depth-dependent storage in the semi-enclosed system but integrated heat redistribution in the open basin. These results demonstrate that basin geometry and circulation regime critically regulate upper-ocean heat storage pathways, with direct implications for regional climate feedbacks, marine heat extremes, and ecosystem vulnerability in rapidly warming subtropical environments.