Three-color electrophoretic displays (EPDs) have the characteristics of colorful display, reflection display, low power consumption, and flexible display. However, due to the addition of red particles, response time of three-color EPDs is increased. In this paper, we proposed a new driving waveform based on high-frequency voltage optimization and electrophoresis theory, which was used to shorten the response time. The proposed driving waveform was composed of an activation stage, a new red driving stage, and a black or white driving stage. The response time of particles was effectively reduced by removing an erasing stage. In the design process, the velocity of particles in non-polar solvents was analyzed by Newton’s second law and Stokes law. Next, an optimal duration and an optimal frequency of the activation stage were obtained to reduce ghost images and improve particle activity. Then, an optimal voltage which can effectively drive red particles was tested to reduce the response time of red particles. Experimental results showed that compared with a traditional driving waveform, the proposed driving waveform had a better performance. Response times of black particles, white particles and red particles were shortened by 40%, 47.8% and 44.9%, respectively.