Graphene/polydopamine aerogels (GPD X AG, where X represents the weight ratio of DA•HCl to GO) were prepared by the chemical reduction of graphene oxide (GO) using dopamine (DA) and L-ascorbic acid as reducing agents. During the gelation process, DA was polymerized to form polydopamine (PDA). The introduction of PDA in the gelation of aerogels led to a deeper reduction of GO and stronger interactions between graphene nanosheets forced by covalent cross-linking and noncovalent bonding including π−π stacking and hydrogen bonding. The weight ratio of DA•HCl to GO influencing the formation and morphology of GPD X AG was explored. With the increasing content of DA in gelation, the reduction of GO and the cross-linking degree of graphene nanosheets were enhanced, and the resulting GPD X AG had a more regular pore distribution. Additionally, introducing PDA into GPD X AG improved its hydrophobicity because of the adhesion of PDA to a network of aerogels. GPD X AG exhibited a higher removal efficiency for organic pollutants than the controlled graphene aerogels (GAG). Specifically, the adsorption capacity of GPD X AG for organic solvents was superior to that of GAG, and organic solvent was completely separated from the oil/water mixture by GPD X AG. The equilibrium adsorption capacity of GPD X AG for malachite green (MG) was measured to be 768.50 mg/g, which was higher than that for methyl orange (MO). In MG/MO mixed solutions, aerogels had obvious adsorption selectivity for the cationic dye. The adsorption mechanism of aerogels for MG was also discussed by simulating adsorption kinetic models and adsorption isothermal models.