The present invention provides a separator for a fuel cell that improves efficiency of the fuel cell by removing water generated in a membrane-electrode assembly and accumulated in a channel of the separator, a manufacturing method thereof, and a fuel cell stack including the same. The separator for the fuel cell of the present invention includes: a main body of a plate shape; a channel concavely formed in at least one surface of the main body and supplying a fuel or oxygen to a membrane-electrode assembly; and a metal layer provided to a surface of the channel and including an oxide layer formed by an anodic oxidation treatment and minute grooves of a nano-scale formed in the oxide layer, thereby forming the surface of the channel to be super-hydrophilic.