The rotaxane-based molecular machines can lead to the appearance of unconventional operations and properties thus, by integrating with aggregation-induced emission (AIE) features to control the construction of polymorphism through supramolecular self-assembly can reach an amazing level of intelligent materials. We rationally described a tris-branched TPE rotaxane RZ3+ of a molecule shuttle, composed of t-butylcalix arene macrocycle, a single axle incorporating ammonium motif, and a bifurcated double strand each containing 1,2,3-triazolium (Tz) cationic unit that terminated with a tetraphenylethene (TPE) stopper. The “concealed” and “exposed” state of the ammonium moiety by a rotaxane RZ3+ is displayed to correspond to opening and closing of the double strand, respectively, which resembles a zipper-like functioning. Distinctive anisotropic nanostructures including nanofibers, nanorods, coarsely truncated shapes, pseudocubes, nanocubes and so on can be forthrightly fabricated by fine tuning the solvent polarity and or the shuttling movement of the macrocycle in THF/water mixture to manipulate the self-assembly processes. Self-assembly reveals that nanocubes can only be constructed by TB3+ and RZ3+ molecules in aqueous media but not by RZ+ and RZ2+ under similar conditions. The fascinating nanocubes was mainly controlled precisely by two major factors i.e., Tz cationic units and aqueous medium. It is worth mentioning that, exotic shape organic nanocubes were seldomly reported in rotaxane-based nano-objects owing to unfavorable thermodynamics for nanocubes formation. This study highlights the benefits of using Tz cationic units, which not only serve as secondary molecular station but also control the self-assembly process to form nanocubes in aqueous medium, providing a new avenue for nanomaterials technology and further enriching the applications of mechanically interlocked molecules (MIMs).