This review focuses on the synthesis and application of nanostructured composites containing magnetic nanostructures and carbon-based materials. Great progress in fabrication of magnetic carbon nanocomposites has been made by developing methods including filling process, template-based synthesis, chemical vapor deposition, hydrothermal/solvothermal method, pyrolysis procedure, sol-gel process, detonation induced reaction, self-assembly method, etc. The applications of magnetic carbon nanocomposites expanded to a wide range of fields such as environmental treatment, microwave absorption, magnetic recording media, electrochemical sensor, catalysis, separation/recognization of biomolecules and drug delivery are discussed. Finally, some future trends and perspectives in this research area are outlined.