The selectivity of electrochemical sensors to ascorbic acid (AA), dopamine (DA), and uric acid (UA) remains an open challenge in the field of biosensing. In this study, the selective mechanisms for detecting AA, DA, and UA molecules on the graphene and graphene oxide substrates were illustrated through the charge population analysis from the DFT calculation results. Our substrate models contained the 1:10 oxygen per carbon ratio of reduced graphene oxide, and the functionalized configurations were selected according to the formation energy. Geometry optimizations were performed for the adsorption of AA, DA, and UA on the pristine graphene, epoxy-functionalized graphene, and hydroxyl-functionalized graphene at the DFT level with vdW-DF2 corrections. From the calculations, AA was bound to both epoxy and hydroxyl-functionalized GO with relatively low adsorption energy, while DA was adsorbed stronger to the electronegative epoxy groups. The strongest adsorption of UA to both types of functional groups corresponded to the largest amount of electron transfer through the pi orbitals of UA. Local electron loss created local electric fields that opposed the electron transfer during an oxidation reaction. Our analysis agreed with the results from previous experimental studies and provide insight into other electrode modifications for electrochemical sensing.