Three-dimensional microstructures play a key role in the fabrication of flexible electronic products. However, the development of flexible electronics is limited in further applications due to low positioning accuracy, the complex process, and low production efficiency. In this study, a novel method for fabricating three-dimensional circular truncated cone microstructures via low-frequency ultrasonic resonance printing is proposed. Simultaneously, to simplify the manufacturing process of flexible sensors, the microstructure and printed interdigital electrodes were fabricated into an integrated structure, and a flexible pressure sensor with microstructures was fabricated. Additionally, the effects of flexible pressure sensors with and without microstructures on performance were studied. The results show that the overall performance of the designed sensor with microstructures could be effectively improved by 69%. Moreover, the sensitivity of the flexible pressure sensor with microstructures was 0.042 kPa−1 in the working range of pressure from 2.5 to 10 kPa, and the sensitivity was as low as 0.013 kPa−1 within the pressure range of 10 to 30 kPa. Meanwhile, the sensor showed a fast response time, which was 112 ms. The stability remained good after the 100 cycles of testing. The performance was better than that of the flexible sensor fabricated by the traditional inverted mold method. This lays a foundation for the development of flexible electronic technology in the future.