S-box is the only nonlinear components of block cipher algorithm which can provide confounding effect. Its password strength determinates the security strength of the whole cipher algorithms. An S-Box generation algorithm based on the discrete chaos system which uses multi-chaos maps and cross-generation method to generate S-Boxes was proposed. Good characteristics such as bounded, aperiodic and extremely sensitive to initial conditions and parameters of discrete chaos system were combined in the algorithm. Experimental analysis shows that the samples generated by our algorithm have strong key sensitivity and good randomness, thus can satisfy both the high security criteria and features required by the S-Box design. It improves the performance by reducing the computational complexity and has good scalability and low implementation cost. Therefore, the proposed method can serve as a promising choice for designing S-Boxes.