Because of the current image encryption algorithm based on the chaotic system exist the negative factor induced by the transient effect, and the pixel diffusion phase of theses algorithm was not using the whole random code sequence, resulting in the low security and not against each plain- and cipher- text attack. So the whole random code sequence and new Jacobian elliptic map were designed in this paper, as well as defining a S-box transformation rule; and constructing the pre-confusion-mixing-diffusion architecture, the image encryption algorithm based on the S-box transformation rule integration with Jacobian elliptic chaotic map was proposed to overcome above defects. Firstly, the S-box transformation rule was used to substitute and permute the pixel of original image; secondly, the external key was generated by the logistic map and algebra transformation function to iterate the Jacobian elliptic chaotic map to eliminate the transient effect, and ignore the results of the iteration; changing the external key, one group of pseudo-random sequence was got by iterating the Jacobian elliptic chaotic map again, and the new sequence was obtained by sequence correction function correcting the pseudo-random sequence to mixing the pixel of pre-confusion image under the condition of mixing mechanism; then the key stream mechanism was used to quantify the correcting sequence to obtain the one-dimension array to encrypt the pixel of mixing image under the condition of diffusion mechanism. This algorithm in paper was test on the platform of MATLAB simulation software; the results showed that the image encryption algorithm has a excellent encryption property such as highly secure, strong key sensitivity, the huge key space to against various kinds of attacks.