The co-assembly of zwitterionic amphiphile and polyoxometalate is a new and promising technique to construct a hierarchical and multifunctional supramolecular hydrogel. To comprehensively investigate the assemble mechanism, zwitterionic amphiphiles with different cations, namely, 3-(1-hexadecyl-3-imidazolio) propanesulfonate (C16IPS) and 3-(1-hexadecyl-2-methyl-3-imidazolio) propanesulfonate (C(16)bIPS), were designed to complex with silicotungstic acid (HSiW). Hydrogen bonding between the oxygen atoms of HSiW and the protons on C-2 of the imidazolium rings and the steric effect significantly influence the morphology and rheological property of the hydrogel. Interestingly, cross-linked worm-like micelles in parallel, vertical, and tilted distribution were observed using cryogenic transmission electron microscopy. In addition, these aggregates were further stacked into hexagonal phases on a large scale. Hence, deep insights into the relationship among the structure of zwitterionic amphiphile, self-assembled architecture, and the mechanical property of a polyoxometalate-based hydrogel were disclosed.