We study protein recognition on a graphene oxide (GO) surface using a single GO piece fixed on a solid support. The GO surface is modified by newly designed processes using pyrene as a linker to an sp2 domain in the GO, an aptamer for thrombin recognition, and a probe dye for fluorescence detection. In this system, the dye probe fluorescence, which was initially quenched by GO, is recovered when the aptamer recognizes the corresponding protein. We demonstrate the label-free and selective protein recognition for thrombin. The elementary processes of protein recognition are observed directly with a confocal laser scanning microscope and an atomic force microscope using an identical piece of GO. They indicate that proteins are recognized homogeneously on the modified GO surface. We also show that the recognition system can be installed and operated in microchannel devices.