The invention provides a nitrogen-doped and carbon-coated magnetic nanoparticle composite microspheres and a preparation method thereof, and belongs to the technical field of materials with an electromagnetic function. According to the method, a glycerin metal complex and a nitrogenous organic compound are taken as main raw materials. A monodispersed glycerin metal complex precursor is prepared according to a self-template method at first; then the surface of the precursor is coated to form a shell by virtue of in-situ polymerization for nitrogenous organic monomers, and a carbon source and anitrogen source are introduced; and finally, calcining is carried out under an inert gas, and a core is subjected to thermal decomposition to form magnetic nanoparticles while the shell is carbonizedto form nitrogen-doped carbon. The nitrogen-doped and carbon-coated magnetic nanoparticle composite microspheres are green and environment-friendly, and efficient and time-saving in preparation process, and suitable for being prepared in a large scale; the electromagnetic parameters of the composite microspheres and the sizes of the magnetic nanoparticles can be regulated and controlled by changing the mass ratio of metal salt to the nitrogenous organic monomers, and an annealing temperature, so that impedance matching and attenuation characteristic are achieved; and the prepared composite microspheres are high in absorption intensity for electromagnetic wave, wide in effective absorption frequency band, easy to prepare in a large scale, and capable of meeting many use needs.