Plasmonic molecules (PMs) composed of polymer-capped nanoparticles represent an emerging material class with precise optical functionalities. However, achieving controlled structural changes in metallic nanoparticle aggregation at the nanoscale, similar to the modification of atomic structures, remains challenging. This study demonstrates the 2D/3D isomerization of such plasmonic molecules induced by a controlled ultrasound process. We used two types of gold nanoparticles, each functionalized with hydrogen bonding (HB) donor or acceptor polymers, to self-assemble into different ABN-type complexes via interparticle polymer bundles acting as molecular bonds. Post-ultrasonication treatment significantly shortens these bonds from approximately 14 to 2 nm by enhancing HB cross-linking within the bundles. This drastic change in the bond length increases the stiffness of the resulting clusters, facilitating the transition from 2D to 3D configurations in 100% yield during drop-casting onto substrates. Our results advance the precise control of PMs' nanoarchitectures and provide insights for their broad applications in sensing, optoelectronics, and metamaterials.