In summary, two series of six-armed amphipathic molecules were designed for the study of the different self-assembly behaviors in water. The slight difference in the flexibility and the length of the linkages leads to completely different self-assembly behaviors. Under similar external conditions, two distinct self-assembly outcomes were observed: the formation of 2D framework structures through the selfassembly of M1 molecules characterized by a rigid and short bridge connecting the hydrophobic core to the hydrophilic edges; alternatively, a 3D cube-like supramolecular cage emerged through the coordinated interaction of six M2 molecules. These M2 molecules were adorned with six hydrophilic and flexible vinyl pyridyl groups, affixed to a hydrophobic hexaphenyl benzene core, facilitated by hydrophobic forces within the aqueous milieu. It was also observed that the various counter anions located in the interlayer of the 2D frameworks play a key role in adjusting the stacking modes relying on a large number of hydrogen bonds between the counter anions and the hydrogen of M1. The SCXRD gave unambiguous evidence of the 2D framework and the 3D cube-like structures. The preparation of well-defined discrete self-assembled structures in water holds immense significance in exploring the fundamental principles of supramolecular chemistry and advancing the understanding of biological systems. In addition, the advantage of designing structurally diverse monomers allows for the fine-tuning of the self-assembled structure and the physical, chemical, and mechanical properties of the resulting supramolecular assemblies.