Low-dimensional van der Waals materials have been extensively studied as a platform with which to generate quantum effects. Advancing this research, topological quantum materials with van der Waals structures are currently receiving a great deal of attention. Here, we use the concept of designing topological materials by the van der Waals stacking of quantum spin Hall insulators. Most interestingly, we find that a slight shift of inversion centre in the unit cell caused by a modification of stacking induces a transition from a trivial insulator to a higher-order topological insulator. Based on this, we present angle-resolved photoemission spectroscopy results showing that the real three-dimensional material Bi4Br4 is a higher-order topological insulator. Our demonstration that various topological states can be selected by stacking chains differently, combined with the advantages of van der Waals materials, offers a playground for engineering topologically non-trivial edge states towards future spintronics applications.