Aiming at the problem of slow convergence and poor effect of GA in solving large-scale sequence optimization problems, a deep evolutionary algorithm is proposed in this work. The algorithm uses the trained network to quickly find the initial solution of the problem and injects the initial solution into the GA population for further optimization. Finally, the optimal solution in the final population will be further optimized by the 2-OPT. The proposed algorithm is compared with other algorithms on the tsplib95 instances and industrial sorting sequence optimization dataset. Experimental results show that the proposed algorithm achieves the best optimization performance compared with other algorithms, especially for large-scale sequence optimization problems.