Controlling the flow of particulate matter, especially nanoparticles, requires a deep understanding of particle structure and motion. In this study, we present experimental observations and intrinsic mechanisms for controlling the nanoparticle flow using vibration-mediated regulation of aggregates evolution. Our findings demonstrate that vibration could exert significant forces on the particles, causing them held apart or would touch with less force and then leads to re-breakup process of the aggregates. Furthermore, the relationship between the vibration parameter, aggregate size, the microchannel size and flow behavior has also been revealed. Notably, the outflowing aggregates have extremely small Stokes numbers due to their high porosity, and their motion is dominated by gas drag. The relationship between particles flow rate and the size of the microchannel and vibration parameters has been identified. These results have significant implications for precise control and assembly of nanoparticles.