The present invention provides a method for manufacturing a composite separator for a fuel cell, which can reduce the electrical contact resistance by performing an additional post-treatment to remove residual resin remaining on the surface of the composite separator by plasma etching. In certain preferred embodiments, the present invention provides a method for manufacturing a composite separator for a fuel cell, in which a liquid phase resin for gasket is applied to the surface of the composite separator along a predetermined gasket pattern, or a semi-cured resin for gasket in the form of a film with a predetermined gasket pattern is stacked on the surface of the composite separator, and then plasma etching is performed to remove the residual resin and, at the same time, cure the resin for gasket, thus reducing the overall processing time to improve the productivity and preventing a composite material of the separator from being damaged.