Microstructure plays an important role in improving the performance of flexible sensors. Changing the shape of the dielectric layer microstructure is an effective countermeasure to promote the sensitivity of capacitive sensors. Nevertheless, traditional microstructure fabrication methods have high manufacturing costs, cumbersome manufacturing processes, and single structure manufacturing, which restrict the development of flexible sensors. In this work, electro-hydro-dynamic (EHD) printing method and aerosol jet (AJ) printing method were applied to fabricate 3D microstructures, in a manner of printing the same pattern in multiple layers. The height and morphology of 3D microstructures, under different printing parameters, were compared by changing the number of printing layers and printing speed. Additionally, the printing effects of the two printing methods were compared. The results demonstrated that various shapes and highly controllable 3D microstructures could be fabricated by both methods. The EHD printing method had higher manufacturing precision, whereas the AJ printing method had higher stacking efficiency. The height and morphology of 3D microstructures could be effectively controlled by changing the number of printed layers and the printing speed of the microstructures. It is indicated that the EHD printing method and the AJ printing method both have great potential in the fabrication of 3D microstructures and that both methods had their own advantages.