During the pipeline plugging process, both the pipeline and the pipe isolation tool (PIT) will be greatly damaged, due to the violent vibration of the flow field. In this study, it was proposed for the first time to reduce the vibration of the flow field during the plugging process by optimizing the surface structure of the PIT. Firstly, the central composite design (CCD) was used to obtain the optimization schemes, and the drag coefficient and pressure coefficient were proposed to evaluate the degree of flow field changes. Secondly, a series of computational fluid dynamics (CFD) simulations were performed to obtain the drag coefficient and pressure coefficient during dynamic plugging. And the mathematical model of drag coefficient and pressure coefficient with the surface structure of the PIT were established respectively. Then, a modified particle swarm optimization (PSO) was applied to predict the optimal value of the surface structure of the PIT. Finally, an experimental rig was built to verify the effectiveness of the optimization. The results showed that the improved method could reduce the flow field vibration by 49.5 6%. This study provides a reference for the design of the PIT surface structure for flow field vibration technology.