During the past decades, the logical model has become a powerful tool in studying and manipulating genetic circuits, motivating much effort on the analysis of logical networks [1, 2]. Correspondingly, the stability, controllability and observability of logical networks have attracted a great deal of attention of biologists, physicists, and systems scientists [3]. Remarkably, many excellent results about the logical networks have been established by using the STP method, of which the main feature is converting logical dynamics into algebraic forms and representing the dynamics of logical networks by Boolean matrices [4]. Another important method to deal with the logical networks is the discrete iteration [5], which together with Boolean matrix theory can be used to explore the relation between the incidence matrix and stability of logical networks. This chapter introduces these two methods and illustrates how to use the Boolean matrices to analyze the logical networks.