Job shop scheduling is an important part of manufacturing process. Pre-mature, local optimal solution or low convergence rate of Genetic Algorithm may come across in solving scheduling problem in multi-Job shop. To avoid those unhealthy tendencies, this paper introduced the Dynamical Niche Sets-based Cooperative Evolutionary Algorithm model.In the Algorithm, Process-based chromosome encoding method was used; the crossover operator and mutation operator were designed to adjust operation sequences and choose process routes. The cooperative scheduling problem in multi-Job shop was solved using dynamical niche sets technology and multi-population cooperative evolution method. The Experiment result shows the proposed method has good advantages.