Biological micro-dissection has a wide range of applications in the field of molecular pathology. The current laser-assisted dissection technology is expensive, and laser radiation can lead to sample contamination. As an economical and pollution-free micro-dissection method, piezoelectric ultrasonic micro-dissection has a wide application prospect. However, the performance of the current piezoelectric ultrasonic micro-dissection technology is unsatisfactory. In this paper, a novel piezoelectric ultrasonic micro-dissection device based on a flexure mechanism is proposed in order to solve the problems of low dissecting precision and excessive wear of the dissecting needle caused by the harmful lateral vibration of the current piezoelectric ultrasonic micro-dissection device. By analyzing the flexibility of flexure hinge, the type of flexure beam and the optimal design parameters are determined. Through comparing the harmonic response simulation analysis of the micro-dissection device based on a flexure mechanism and the traditional micro-dissection device without the flexure mechanism, the newly designed micro-dissection device achieves the best vibration effect when the driving frequency is 28kHz, compared with the traditional micro-dissection device, the lateral vibration suppression effect is improved by 68%. Then, based on the 3D printing technology, a prototype of a novel micro-dissection device was produced, and its performance was tested. It was found that the flexure mechanism did indeed suppress the lateral vibration of the needle tip. Finally, the experiments of 5μm thick paraffin-embedded rat liver sections were carried out, and the effects of different dissecting parameters on the dissecting effect were analyzed, and the optimal dissecting parameters were obtained. By comparing the dissecting effects of the tissue sample and the wear condition of the needle tip between the novel micro-dissection device and the traditional micro-dissection device under their optimal dissecting parameters, it is proved that the suppression of harmful lateral vibration not only significantly improves the dissecting effect, but also improves the service life and durability of the dissecting needle, which is beneficial to reduce the equipment costs.