In this work, the impact of heat treatment on the real structure of Bi2Te3/Sb2Te3 multilayers is investigated. The material was heated in situ in the transmission electron microscope (TEM) and ex situ inside a furnace after preparing these layers with the so-called nanoalloying deposition technique via molecular beam epitaxy (MBE) equipment. The samples were prepared as a lamella for TEM studies using focused ion beam technique. EDX elemental mapping and high angle annular dark field mode-STEM were performed to monitor changes of the morphology and interdiffusion phenomena after heating up to 250 °C. A grain growth started during heating and the chemical layer structure was smeared out partly but remained in several grains and was found to be adjusted parallel to a major lattice plane in a crystallite. High resolution TEM shows polysynthetic twinning in a number of crystals.