Controlling the assembly and manipulating the oxidation state of graphene nanosheets on surfaces are of essential importance for application of graphene-related optical and biosensing devices. In this study, we assemble a graphene oxide (GO) film on a surface plasmon resonance chip surface and then convert it to reduced graphene by an in situ electrochemical method. The mechanism and application of surface-enhanced Raman spectroscopy and DNA sensing from graphene-based substrates are investigated. The average thickness and dielectric constant of GO are varied significantly with the switch of its oxidation state. Electrochemical reduction decreases the distance between carbon atoms and the gold surface by removing the spacer of oxygen functional groups. The electromagnetic field of the graphene surface is therefore enhanced, resulting in an enhancement of the Raman signal. A p doping of electrochemically reduced GO (ERGO) that occurred from changes in the graphene electronic structure through interaction between gold and ERGO is also observed during electrochemical reduction. The GO and ERGO substrates perform different interaction abilities with single- and double-stranded DNA. This work may be valuable for graphene-related research works on optoelectronics and biosensors.