Exploration of the structure formation and dynamics of animate and inanimate matter on the nanometer scale is a highly interdisciplinary field of rapidly emerging research. It is relevant for various molecular and nanoscale systems of different origins and compositions and concerns numerous phenomena originating from physics, chemistry, biology, and materials science. This topical issue presents a collection of research papers devoted to different aspects of the Dynamics of Systems on the Nanoscale. Some of the contributions discuss specific applications of the research results in several modern and emerging technologies, such as controlled nanofabrication with charged particle beams or the design and practical realization of novel gamma-ray crystal-based light sources. Most works presented in this Topical Issue were reported at the joint Sixth International Conference "Dynamics of Systems on the Nanoscale" and the tenth International Symposium "Atomic Cluster Collisions" (DySoN-ISACC 2021), which were held