Flow shop scheduling problems are NP-hard problems. Heuristic algorithms and evolutionary metaheuristic algorithms are commonly used to solve this kind of problem. Although heuristic algorithms have high solving speed, the solution quality is not good. Evolutionary algorithms make up for this defect in small-scale problems, but the solution performance will deteriorate with the expansion of the problem scale and there will be premature problems. In order to improve the solving accuracy of flow shop scheduling problems, a computational efficient optimization approach combining NEH and niche genetic algorithm (NEH-NGA) is developed. It is strengthened in the following three aspects: NEH algorithm is used to optimize the initial population, three crossover operators are used to enhance the genetic efficiency, and the niche mechanism is used to control the population distribution. A concrete application scheme of the proposed method is introduced. The results of compared with NEH heuristic algorithm and standard genetic algorithm (SGA) evolutionary metaheuristic algorithm after testing on 101 FSP benchmark instances show that the solution accuracy has been significantly improved.