Improving the desalination performance of membranes is always in the spotlight of scientific research; however, Janus channels with polarized surface charge as nanofiltration membranes are still unexplored. In this work, using molecular dynamics simulations, we demonstrate that Janus graphene oxide (GO) channels with appropriate geometry and surface charge can serve as highly efficient nanofiltration membranes. We observe that the water permeability of symmetric Janus GO channels is significantly superior to that of asymmetric channels without sacrificing much ion rejection, owing to weakened ion blockage and electrostatic effects. Furthermore, in symmetric Janus GO channels, the transport of water and ions is sensitive to the charge polarity of the channel inner surface, which is realized by tuning the ratio of cationic and anionic functionalization. Specifically, with the increase in cationic functionalization, the water flux decreases monotonously, while ion rejection displays an interesting maximum behavior that indicates desalination optimization. Moreover, the trade-off between water permeability and ion rejection suggests that the Janus GO channels have an excellent desalination potential and are highly tunable according to the specific water treatment requirements. Our work sheds light on the key role of channel geometry and charge polarity in the desalination performance of Janus GO channels, which paves the way for the design of novel desalination devices.