The study of cellular networks is one of the hot research topics in systems biology. Combining computational network models with experiment techniques, researchers can analyze complex biological systems from a systemic perspective, and provide new hypothesis and guidance for biological discovery. In the last ten years, many methods for the reconstruction and analysis of genome-scale metabolic networks, gene regulatory networks and signal transduction networks have been developed. The integration of these different types of biological networks is becoming a new research hotspot recently. The study of integrated network raises many new challenges. In this paper, we reviewed the methods for the reconstruction and analysis of integrated networks, with a particular focus on the integrative models of metabolic and transcriptional regulatory networks as most researches are on this type of integrated networks. We first gave a brief introduction of the different cellular networks, and then discussed the reconstruction methods and the application of integrated networks. In the end, the problems and future development directions were also discussed．