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The paper presents an effective method for different structure digital system based on on-line evolution with fault tolerance technology. Integer-coding multistage evolution is used to design digital system and different-structure system is evaluated by using the knowledge of quad tree. Thus, the length of chromosome can be reduced and the degree of different structure system can be evaluated effectively. The on-line evolutionary design of a 4×2 multiplier was performed as an example, and the experimental results showed that, compared with the existing methods, the digital circuit was successfully on line evolved and the fault-ability of the different-structure redundant systems was raised.