Controlling the nanostructure of conducting polymers (CPs) is essential for enhancing their performance in energy storage applications. Existing CPs often suffer from low effective pseudocapacitance due to poor ion permeability. In this study, we introduce a novel approach using hydrogen-bonded organic frameworks (HOFs) to synthesize porous poly(3,4-ethylenedioxythiophene) (PEDOT). By leveraging the flexible hydrogen-bonding interactions, we incorporated 3,4-ethylenedioxythiophene (EDOT) into HOF-16. Following in situ polymerization of EDOT, the HOF-16 was removed to form a porous, interconnected network of PEDOT. Electrochemical evaluations demonstrated that the porous PEDOT exhibited significantly enhanced performance, including high specific capacitance, excellent rate capability, and ~95% capacitance retention after 10,000 cycles. Compared to PEDOT without HOF, the porous PEDOT showed a 34% increase in specific capacitance and a 10% improvement in 10,000-cycle capacitance retention. This work highlights the potential of HOF-enabled synthesis in creating high-performance conducting polymers, offering a new avenue to improve supercapacitor performance, particularly in terms of capacitance and stability.