Production scheduling of semiconductor wafer manufacturing is a challenging research topic in the field of industrial engineering. Based on this, the green manufacturing collaborative optimization problem of the semiconductor wafer distributed heterogeneous factory is first proposed, which is also a typical NP-hard problem with practical application value and significance. To solve this problem, it is very important to find an effective algorithm for rational allocation of jobs among various factories and the production scheduling of allocated jobs within each factory, so as to realize the collaborative optimization of the manufacturing process. In this paper, a scheduling model for green manufacturing collaborative optimization of the semiconductor wafer distributed heterogeneous factory is constructed. By designing a new learning strategy of initial population and leadership level, designing a new search strategy of the predatory behavior for the grey wolf algorithm, which is a new swarm intelligence optimization algorithm proposed in recent years, the diversity of the population is expanded and the local optimum of the algorithm is avoided. In the experimental stage, two factories’ and three factories’ test cases are generated, respectively. The effectiveness and feasibility of the algorithm proposed in this paper are verified through the comparative study with the improved Grey Wolf Algorithms—MODGWO, MOGWO, the fast and elitist multi-objective genetic algorithm—NSGA-II.