Abstract: S-boxes are the only nonlinear component in many cryptographic algorithms, which decides the secutity strength of the whole algorithm. S-boxes with good cryptographic properties can be constructed by genetic algorithm, and it is proved in practice that optimizing cryptographic propertie of S-boxes in the middle procedure of algorithm can make the algorithm more effective. Difference uniformity is also an important aspect to weigh S-boxes. How to improve difference uniformity with difference matrix is considered. And a practical algorithm is given, which can improve nonlinearity and difference uniformity of a randomly chosen bijective S-box simultaneously.