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Controlling nanoscale heat generation, dissipation, and transport is crucial for miniaturizing electronic devices and for designing highly efficient thermoelectric materials. However, it has been challenging to directly measure thermal properties at individual atom level. Herein, direct atomic‐resolution column‐by‐column imaging of the rattling motion of Ba atoms in a clathrate compound Ba8Ga16Ge30 using atomic‐resolution scanning transmission electron microscopy with a segmented detector is shown. The directional anisotropy of the rattling motion is clearly visualized in real space and its amplitude and anisotropy are quantitatively evaluated by Bayesian analysis of the thermal diffuse scattering distribution. These results open a new possibility for directly characterizing nanoscale thermal properties in materials and devices, even those containing heavy elements such as thermoelectric materials.