Aiming at designing a high safe and high efficiency cryptosystem, the period of the sequence cipher can not be too long, and the cipher sequence produced should approach random numbers. But the key sequence produced by traditional methods sometimes does not have randomness, which makes insecurity the system using this key sequence. Considering this, in this paper, we take two criteria usually used to evaluate the randomness of a key sequence as two objectives of Multi-Objective Evolutionary Algorithm (MOEA), and a new sequence cipher producing method based on two-layer MOEA is proposed (called TLEASCP). Because of TLEASCP is based on the randomness of crossover operator and mutation operator of the high efficient MOEA, the key sequences produced by TLEASCP have the merits of high randomness, chaos and long period.