This paper considers the practical manufacturing environment of the hybrid flow shop (HFS) with non-identical machines in parallel. In order to significantly enhance the performance level of manufacturing, maintaining load balancing among parallel machines is very important. The aim of this paper is to minimize makespan with load balancing in a non-identical parallel machine environment by using hybrid genetic algorithm (HGA). In the HGA, the neighborhood search-based method is used together with genetic algorithm as local optimization method to balance the exploration and exploitation abilities. The representation of chromosome used in this paper is composed of two layers: allocation layer and sequencing layer, which can be encode and decoded easily. In generating initial population, a special constraint of load balancing between parallel machines is used to reduce the number of individuals. And particular crossover operation is used, which generates multiple offspring at a time, so that the efficiency of the algorithm can be well improved. At last, the proposed algorithm is tested on a benchmark, and numerical example shows good result.