In order to apply ultrasonic particle manipulation technology to the aggregation of nano-drug particles in blood vessels， and aiming at the influence of flow rate and the spontaneous agglomeration of nanoparticles due to the nano effect， the theoretical calculation model of nanoparticle aggregation by focused ultrasound under flow rate disturbance is established using the COMSOL finite element software， based on the piezoelectric equation， the acoustic-structure boundary coupling equation， and the momentum equation. Through the comparison and analysis of simulation calculations and experimental results， the reasons for the aggregation of nanoparticles by focused ultrasound are obtained. The explanation theory of nanoparticle cluster intervention and the influence law of local flow rate changes under the interference of flow are also analyzed. It is proved that the nanoparticles liquid in the closed pipeline can be aggregated by focused ultrasound， which shows a certain binding ability to the nanoparticle clusters while the flow rate is less than 1.92 mm/s， providing a new method and approach for future targeted drug therapy.