We report a new synthesis approach for the precise control of wall morphologies of colloidal polypyrrole microparticles (PPyMPs) based on a time-dependent template-assisted polymerization technique. The resulting PPyMPs are water processable, allowing the simple and direct fabrication of multilevel hierarchical PPyMPs films for energy storage via a self-assembly process, whereas convention methods creating hierarchical conducting films based on electrochemical polymerization are complicated and tedious. This approach allows the rational design and fabrication of PPyMPs with well-defined size and tunable wall morphology, while the chemical composition, zeta potential, and microdiameter of the PPyMPs are well characterized. By precisely controlling the wall morphology of the PPyMPs, we observed a pure nanoscale morphological effect of the materials on the energy storage performance. We demonstrated by controlling purely the wall morphology of PPyMPs to around 100 nm (i.e., thin-walled PPyMPs) that the thin-walled PPyMPs exhibit typical supercapacitor characteristics with a significant enhancement of charge storage performance of up to 290% compared to that of thick-walled PPyMPs confirmed by cyclic voltametry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy. We envision that the present design concept could be extended to different conducting polymers as well as other functional organic and inorganic dopants, which provides an innovative model for future study and understanding of the complex physicochemical phenomena of energy-related materials.