Abstract The heat content in the Indian Ocean has been increasing owing to anthropogenic greenhouse warming. Yet, where and how the anthropogenic heat is stored in the Indian Ocean have not been comprehended. Analysis of various observational and model-based datasets since the 1950s reveals a robust spatial pattern of the 0–700 m ocean heat content trend (ΔOHC), with enhanced warming in the subtropical southern Indian Ocean (SIO) but weak to minimal warming in the tropical Indian Ocean (TIO). The meridional temperature gradient between the TIO and SIO declined by 16.4% ± 7.5% during 1958–2014. The heat redistribution driven by time-varying surface winds plays a crucial role in shaping this ΔOHC pattern. Sensitivity experiments using a simplified ocean dynamical model suggest that changes in surface winds over the Indian Ocean, particularly those of the SIO, caused a convergence trend in the upper SIO and a divergence trend in the upper TIO. These wind changes primarily include the enhancements of westerlies in the Southern Ocean and the subtropical anticyclone in the SIO. Albeit with systematic biases, the ΔOHC pattern and surface wind changes simulated by phase 6 of the Coupled Model Intercomparison Project (CMIP6) models broadly resemble the observation and highlight the essence of external forcing in causing these changes. This heat storage pattern is projected to persist in the model-projected future, potentially impacting future climate.