For current multi-image encryption system of joint transform correlator (JTC), the quality of decryption image is not good when encrypting or decrypting gray image, thus in this paper, a JTC multi-image encryption system based on binary coding for gray images is designed. The system converts the problem of encrypting gray multi-image into the problem of encrypting binary multi-image, which can effectively suppress the unsaturated noise generated during the process of encryption and improve the quality of decrypted images. The simulation results show that the correlation coefficent of the decryption image using the binary coding image of the gray image is significantly improved in the JTC multi-image encryption system based on spiral phase masks' topological charge number multiplexing. Then the quality of the decrypted image can be further improved by using the median filtering to suppress the saturation noise in the decrypted image.