During the space electronic system in carries out the exploratory mission in the deep space, it maybe faced with kinds of violent natural environment, to electric circuit's performance, the volume, the weight and the stability proposed a higher request, the traditional circuit design method already more and more with difficulty satisfied this kind of request. The traditional circuit design method already more and more with difficulty satisfied this kind of request. But unifies the programmable component and the evolutionary algorithms hardware may the dynamic change hardware's structure adapt the adverse circumstance, resume the damage of the function, the adaptation for the duty change. After the optimization, obtains the circuit structure will often stem from our anticipation, this will be the altitude which the experience and the skillful institute hope to attain with difficulty. In view of the Xilinx Company's FPGA unique feature, proposed one kind of evolutionary algorithms which uses in the space electronic system circuit optimization design and through the experiment proved, the algorithm obtains the circuit structure to surpass the tradition circuit design method. This work investigates the application of genetic algorithms in the field of circuit optimization. For the case studies, this means has proved to be efficient and the experiment results show that the new means have got the better results.