To mitigate reliance on operators during fundus imaging, an automated rapid localization and alignment method for the human pupil using visible light pupil imaging was proposed. Initially, the pupil alignment device was constructed on a laboratory fundus imaging system using a visible light camera module and a three-dimensional electric displacement stage. Subsequently, the effective area of the image was extracted using the Hough gradient method to determine the center of the fundus imaging system. The pupil region was identified through the maximum inter-class variance method and image histogram feature, while the center of the pupil was ascertained via the minimum circle fitting method. Ultimately, the electric displacement stage's movement is regulated through feedback mechanisms, ensuring that the center of the fundus imaging system aligns precisely with the pupil's center. The experimental results show that the average recognition speed of human pupil is 0.11 s, the average recognition accuracy of the pupil center is 98.7%, and the average Euclidean distance of the center deviation is 4.3 pixels. It can satisfy the system requirements of the real-time and accuracy, and provides an efficient automatic pupil alignment solution for fundus imaging system.