We report ambivalent rejection behavior of a graphene oxide membrane (GOM) having a reduced interlayer spacing. Ultrathin GOMs having a thickness of 50 nm were fabricated using a vacuum filtration method followed by subjecting the samples to thermal reduction at 162 °C. The interlayer spacing of GOMs was reduced by 1 Å on thermal reduction as compared with that of the natural GOMs. The rejection rate with dye molecules was tested using dyes having three different types of charges in a dead-end filtration instrument. Rejection rate of the reduced GOM with the dyes having an opposite charge was improved up to 99.7%, indicating the dominant effect of the physical sieving diameter. In contrast, in the case of ion permeation of natural GOM, a higher rejection rate for several metal ions was observed as compared with that of GOMs having 1 Å smaller interlayer spacing, indicating the dominant effect of surface charges on the GOM samples.