Motile cilia composed of 9+2 axonemes generate coordinated beats to propel directional fluid flows for various physiological functions. This requires multiciliated cells to establish translational, rotational and planar polarities. However, the mechanism underlying the establishment of these polarities remain elusive. Here, we delve into the functions of mammalian kinesin-9 family and uncover that Kif6, but not Kif9, is critical for establishing both rotational and planar polarities. Kif6 associates with intraflagellar transport (IFT) pariticles and participates in IFT within motile cilia. Knockout of Kif6 leads to severe hydrocephalus due to disruptions in both rotational and tissue-level polarity across ependyma. Conversely, while Kif9 is proposed as a central pair kinesin, its depletion does not significantly affect ependymal cilia motility, although ventricular expansion and defective sperm motility are observed. These findings reveal the unique roles of Kif6 and Kif9 in regulating cilia/flagella beating, providing valuable insights into the complex regulatory mechanisms governing the polarity of multiciliated tissues and the motility of cilia/flagella.