There is a growing interest in miRNA-miRNA synergistic regulations and the relationships between miRNAs and Subpathway regulated by the miRNA to understand the mechanisms of complex diseases.Complex diseases are affected by several miRNAs rather than a single miRNA.So, it is a challenge to identify miRNA synergism for further elucidating miRNA functions at a system-wide level and explore disease miRNAs features in the miRNA-miRNA synergistic network and miRNAs and subpathways network from a new view.In this talk we present a framework for constructing the miRNA-miRNA functional synergistic network (MFSN) and miRNAs and subpathways network (MSN).we investigated the properties of MFSN and MSN in the complex diseases conditions.We further revealed the topological features of disease miRNAs in the MFSN are distinct from non-disease miRNAs.They have more synergism indicating their higher complexity of functions and are the global central cores of the MFSN.In addition, miRNAs for the same disease are close with each other.It also showed that the MSN based analysis not only provided a global view on the relationship among disease, miRNA and subpathway, but also uncovered the function aspects of miRNA regulations and potential pathogenesis of complex diseases .