Gel electrophoresis techniques have been commonly applied in sieving plasmonic nanoparticle oligomers, while the intrinsic role in determining their phoresis velocity differences through the gel remains debatable. In this work, we explore the components and yield in each gel band after bundling two rationally designed types of nanoparticles in a system for electrophoretic separation. All results indicate that the mass property of plasmonic oligomers plays an essential role in determining their phoresis velocity divergences during separation. Further theoretical simulations reveal that the grounds for the mass-determining role stemmed from the random inelastic collisions among the oligomers and the gel-network microchannel. Moreover, under the guidance of such a mass-determining role, it is easy to achieve the direct electrophoretic separation of hetero-structured plasmonic dimers with high purity and high yield. This work will not only facilitate the precise nano-engineering of complex plasmonic oligomers with unique optical properties, but also might remove the obstacles toward their industrial manufacture with high purity.