Microbial metabolic engineering and synthetic biology are important disciplines of microbial technology nowadays. Microbial cells are fast growing, easy to be cultivated in large scale, clear in genetic background and convenient in genetic modification. They play an important role in many domains. Microbial cell factory means an artificial microbial metabolic system that can be used in chemical production. The construction of a microbial cell factory needs transferring of multiple genes or a whole metabolic pathway, which may cause some problems such as metabolism imbalance and accumulation of mesostates. This review focuses on the regulation strategies of different levels involving simultaneous engagement of multiple genes. Future perspectives on the development of this domain were also discussed.