One aspect of the disclosed is to provide a method of manufacturing a nanoporous multilayer graphene membrane, including a first step of oxidizing a surface of a multilayer graphene membrane, a second step of reducing the oxidized surface of the multilayer graphene to carry out reductive etching such that oxidized carbon atoms on the surface are naturally and randomly dispersed, and a third step of repeatedly performing a series of the first and the second steps until nanopores penetrating the multilayer graphene are formed.