One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism,while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.