Septins, components of the fourth cytoskeleton, play an indispensable role in establishing and maintaining epithelial cell polarity. However, the molecular mechanisms underlying the dynamic assembly of higher-order septin structures and the establishment of epithelial cell polarity remain elusive. Here, we show that septins form a previously unrecognized dynamic structure with liquid-like properties in polarized Madin–Darby canine kidney cells. We identified Septin 6 (SEPT6) as the key human septin that undergoes liquid–liquid phase separation (LLPS) both in vitro and in vivo through weak, multivalent interactions mediated by its C-terminal tail. SEPT6 mutants defective in LLPS in vitro also fail to support adherens junction integrity and cell polarity establishment in 2D and 3D cell cultures. Our findings indicate that weak, multivalent interactions are essential for the assembly of higher-order septin structures in cells. We propose that these interactions, in conjunction with conventional interactions between folded domains, generate partially ordered septin assemblies that support the apical–basal axis and lumen formation in metazoans.