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Three-dimensional (3D) nanostructured conducting polymer hydrogels represent a group of high-performance electrochemical energy-storage materials. Here, we demonstrate a molecular self-assembly approach toward controlled synthesis of nanostructured polypyrrole (PPy) conducting hydrogels, which was "cross-linked" by a conjugated dopant molecule trypan blue (TB) to form a 3D network with controlled morphology. The protonated TB by ion bonding aligns the free sulfonic acid groups into a certain spatial structure. The sulfonic acid group and the PPy chain are arranged by a self-sorting mechanism to form a PPy nanofiber structure by electrostatic interaction and hydrogen bonding. It is found that PPy hydrogels doped with varying dopant concentrations and changing dopant molecules exhibited controllable morphology and tunable electrochemical properties. In addition, the conjugated TB dopants promoted interchain charge transport, resulting in higher electrical conductivity (3.3 S/cm) and pseudocapacitance for the TB-doped PPy, compared with PPy synthesized without TB. When used as supercapacitor electrodes, the TB-doped PPy hydrogel reaches maximal specific capacitance of 649 F/g at the current density 1 A/g. The result shows that PPy nanostructured hydrogels can be tuned for potential applications in next-generation energy-storage materials.