High‐quality aluminum (Al) /silicon (Si) heterojunction is crucial in a wide range of applications, such as superconductivity, interfacial heat exchanging, interconnection of Si‐based transistors, etc. However, serious Al/Si heterointerface degradation has been observed when operating at relatively higher temperatures. Understanding the interfacial atomic diffusion is thus a vital step for improving the Al/Si interface quality. We report the atomic diffusion behavior at an epitaxial Al/Si interface via in‐situ heating in Cs‐corrected scanning transmission electron microscopy (STEM). After heating to 493 ± 20 K, the Al/Si interface gradually migrates towards the Al side. This interfacial atomic migration is more active along grain boundaries due to weaker bonding between atoms caused by misorientation of grains. The new interface exhibits a trapezoidal shape, characterized by a slanted smooth left facet and a stepped right facet. This distinct morphology is attributed to minimizing the interfacial energy. Additionally, the migrated Si atoms tend to form a new nanocrystal following the initial lattice orientation in Al, while the diffused Al atoms are usually randomly inserted into the Si lattice matrix among a large region, which can be attributed to lower bonding energy of Al compared with Si.This article is protected by copyright. All rights reserved.