A novel nanoparticle, magnetic graphene quantum dot (MGQD), was synthesized by hydrothermally cutting graphene oxide-iron oxide sheet for contrast agent in magnetomotive optical coherence tomography (MMOCT) and confocal fluorescence microscopy (CFM). The MGQD has superparamagnetism, which allows the MGQD to be tracked and imaged using MMOCT. The MMOCT can display paramagnetic nanoparticle in vivo and provide an anatomical information with micron scale resolution and long imaging depth in clinic application. Moreover, the MGQD has excitation-depend fluorescence and emits visible fluorescence under the excitation of 360nm light, which allows the MGQD to be used as tracer in CFM. CFM can offer intracellular details due to higher resolution, while CFM is unsuitable for imaging anatomical structure because of the limited view of field. The use of MGQD for cell or tissue tracking realizes the combination of MMOCT and CFM, and gives a more comprehensive diagnosis.