By the self-assembly between citrate-stabilized Au nanoparticles (NPs) and dedoped montmorillonite (MMT)/polyaniline (PANI) core/shell nanoflakes, Au NP/MMT/PANI nanoflakes could be fabricated facilely. Importantly, hydrogen bonding between Au NPs and the PANI shell of MMT/PANI nanoflakes was proposed to play a pivotal role in driving that self-assembly. The as-prepared product exhibited high catalytic activity when the reduction of p-nitrophenol was taken as a model reaction. These novel findings of the self-assembly mechanism and the preparation process of Au/MMT/PANI nanocatalyst may shed some light on designing and preparing other functional Au NP/conducting polymer composites by self-assembly.