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Compared with thrombus dissolution using only thrombolytic agents, an advanced therapy of direct stirring of the blood clot can yield shorter recanalization time and higher recanalization velocity. Our previous research presented the design of a novel micro-stirrer, which can convert longitudinal vibration into transverse vibration and eventually generate opposite transverse vibration at the end-effort, like a scissor, for efficient blood clot stirring and thrombus dissolution acceleration. Transverse vibration is the most effective movement to dissolve thrombi. However, the small size of blood vessels has strict limits, which will greatly affect the output transverse vibration. Therefore, to improve the output performance of the micro-stirrer in curved and narrow vascular spaces, the analysis and structure optimization of the micro-stirrer is expected to increase the vibration mode conversion efficiency from longitudinal to transverse mode. The design concept and theoretical analysis of the micro-stirrer are presented in detail. Aiming to obtain the optimal structure parameters of the micro-stirrer, the mathematical model is established and analyzed. Next, a series of finite element models involving important structure parameters are designed and investigated. Finally, the optimal structure parameters are obtained, and the stirring effect in a blood vessel is verified by simulation and experiment.