Biological microdissection has a wide range of applications in the field of molecular pathology. The current laser-assisted dissection technology is expensive. As an economical microdissection method, piezoelectric ultrasonic microdissection has broad application prospects. However, the performance of the current piezoelectric ultrasonic microdissection technology is unsatisfactory. This paper aims to solve the problems of the low dissecting precision and excessive wear of the dissecting needle caused by the harmful lateral vibration of the present piezoelectric ultrasonic microdissection device. A piezoelectric ultrasonic microdissection device based on a novel flexure mechanism is proposed. By analyzing the flexure hinge flexibility, the type of flexure beam and the optimal design parameters are determined. Through harmonic response simulation analysis, the newly designed microdissection device with a vibration-suppressing mechanism achieves the best vibration effect when the driving frequency is 28 kHz. Under this driving frequency, the lateral vibration suppression effect is improved by 68% compared to the traditional effect without vibration suppression. Then, based on 3D printing technology, a prototype of a novel microdissection device is produced, and its performance is tested. Experiments on dissecting needle vibration tests show that the flexure mechanism does indeed suppress the lateral vibration of the needle tip. We conducted various tissue dissection experiments on paraffin tissue sections. First, we determine the optimal dissecting parameters (driving voltage, frequency, feed speed, cutting angle) of the new equipment through various parameter dissecting experiments. Then, we adopt these optimal dissecting parameters to perform three kinds of dissecting experiments on mouse tissue paraffin section (liver, lung, bone), dissecting experiments on tissue sections of different thicknesses (3 μm, 4 μm, 5 μm), sampling and extraction experiments on complete tissue. The new device has a better dissecting performance for paraffin tissue sections below a 5 μm thickness and can complete various dissecting tasks. Finally, we compare the wear of the dissecting needles of the new and old devices after the same dissecting tasks. The results prove that the suppression of harmful lateral vibration not only significantly improves the dissecting effect but also increases the service life and durability of the dissecting needle, which is beneficial for reducing the equipment costs.