The multi-channel reduced graphene oxide membranes with separation function have been synthesized by a simple hydrothermal reduction method and vacuum filtration. In the as-synthesized membranes, the size, number, and type of the nanochannels can be controlled by the reduced temperature. The flux and retention rate of solution are investigated by filtering different size dye molecules. The interception and adsorption effect in the separation process are discussed. Furthermore, the sizes of the nanochannels in the membranes prepared by the different reduced temperatures are estimated. The results indicate that the multi-channel reduced graphene oxide membranes have potential application in water purification area.