A three-dimensional reduced graphene oxide aerogel with embedded nickel oxide nanoparticles was prepared by a one-step self-assembly reaction in a short time. The nanoparticles could be captured into the interior of reduced graphene oxide network during the formation of the three-dimensional architecture. The composite exhibited porosity, good biocompatibility, and abundant metal affinity binding sites. The aerogel was used to isolate ovalbumin selectively from egg white, and favorable adsorption was achieved at pH 3. An adsorption efficiency of 90.6% was obtained by using 1 mg of the composite for adsorbing 70 μg/mL of ovalbumin in 1.0 mL of sample solution, and afterwards a recovery of 90.7% was achieved by using an eluent of 1.0 mL Britton-Robinson buffer solution at pH 5. After the adsorption/desorption, ovalbumin showed no change in the conformation. The adsorption behavior of ovalbumin on the reduced graphene oxide composite well fitted to the Langmuir adsorption model, and a corresponding theoretical maximum adsorption capacity was 1695.2 mg/g. A sodium dodecyl sulfate polyacrylamide gel electrophoresis assay demonstrated that the aerogel could selectively isolate ovalbumin from chicken egg white.