Constipation is very pervasive all over the world. It is a common multifactorial gastrointestinal disease, and its etiology and pathomechanism are not completely clear. Now, increasing evidence shows that intestinal flora is closely related to constipation. Intestinal flora is the largest microbiota in the human body and has powerful metabolic functions. Intestinal flora can produce a variety of metabolites, such as bile acids, short-chain fatty acids, tryptophan metabolites, and methane, which have important effects on intestinal motility and secretion. The host can also monitor the intestinal flora and regulate gut dysbacteriosis in constipation. To explore the relationship between intestinal flora and host, the combination of multiomics technology has become the powerful and effective method. Furthermore, the homeostasis restoration of intestinal flora also provides a new strategy for the treatment of constipation. This review aims to explore the interaction between intestinal flora and host in constipation, which contributes to disclose the pathogenesis of constipation and the development of novel drugs for the treatment of constipation from the perspective of intestinal flora. KEY POINTS: • This review highlights the regulation of gut microbiota on the intestinal motility and secretion of host. • The current review gives an insight into the role of the host on the recognition and regulation of intestinal ecology under constipation. • The article also introduces some novel methods of current gut microbiota research and gut microbiota-based constipation therapies.