Herein, we realized the supramolecular confinement of a single polyoxometalate (POM) cluster precisely in a polypyrrole (PPy) hydrogel-wrapped CNT framework with molecular-scale cages. This hybrid hydrogel framework demonstrated an ultra-high loading (67.5 wt%) and extremely uniform dispersion of individual of H3[P(Mo3O10)4] (PMo12) molecules, as demonstrated by sub-ångström-resolution HAADF-STEM. Consequently, it exhibited a better supercapacitor performance than that of the conventional composite system. The flexible solid-state supercapacitor exhibited a high energy density of 67.5 μW h cm-2 at a power density of 700 μW cm-2 and delivered a high capacitance retention of 85.7% after 3000 cycles. Moreover, the flexible device exhibited excellent mechanical stability. Density functional theory calculations revealed that the wrapped "fishnet-like" hydrogel creates a cage structure with a size of 1.8 nm for the precise storage of the PMo12 molecule (diameter = 1.05 nm), leading to the mono-dispersion of single PMo12 molecules on the hybrid hydrogel. The "caging" effect also activates the PMo12 molecule to enhance its charging/discharging performance by introducing new reactive sites for proton transfer. We believe that this design for suitable cage structures can be used for the construction of other POM-based hybrid hydrogels, thereby achieving mono-dispersity and performance enhancement.