In this paper, a new gray image encryption system based on 3D chaotic map and deoxyribonucleic acid (DNA) sequence operations is presented. SHA is designed to give the initial value of the encryption system. The whole algorithm is designed based on permutation and diffusion framework. First, modify the chaotic sequence generated by the chaotic system, and the Arnold function is permuted the plane image. Secondly, DNA level diffusion is introduced, we start by performing a DNA XOR on the DNA coding image. Lastly, decoding is performed on the diffused DNA matrix. The results of experiment and analyses indicate that our encryption algorithm can pass the attack tests and has a certain application prospect.