In this paper, built mathematical model on Flow Shop scheduling, put forward a RNA genetic algorithm based on DNA computing to solve the Flow Shop scheduling problems. Adopt RNA four digit system encoding method based on DNA computing and RNA computing operator in genetic algorithm. It resolved the encoding scheme and convergence problem which exists in the conventional genetic algorithm. Under some constraint conditions, this genetic algorithm got simulated. Simulation results showed that this algorithm has a better optimum searching and seeking abilities, made the scheduling results comparatively reasonable and expanded the application of DNA computing.