Abstract: Gene regulatory network is the complex regulatory information between a lot of genes which was regulated by some transcriptional factors and carried out biological function with expressing relation proteins at last, it is very important for researchers to understand biological processes and gene function. To understand regulatory mechanism of gene in regulatory network, it is necessary to research topological structure and organization. It not only can illuminate the local characters of the network, but also can reveal the constructing methods of it, what’s more, the research work can also analyze regulatory pathway completely and systemically. Now, more and more researchers approbate the hierarchy structure of gene regulatory network. Here, we discuss the middle two level of the hierarchy: motif and module, and then compare various research on network organization brought out within several years, explaining the biology signification of each one, giving out the disadvantages and problems. Basing on the problems, we also bring up some possible research direction, and then paint the prospect of gene regulatory network modular organization.