The work aims to prepare magnetic graphene and achieve its alignment, in order to provide a directional thermal phase for further preparation of well-formed thermal interface materials. By means of polymer cladding and layer-by-layer assembly technique, the graphene surface uniformly was coated with a negatively charged polystyrene sulronate (PSS) polyelectrolyte layer firstly, and then under the action of electrostatic force, it was coated with a layer of positively charged poly diallyldimethyl ammonium chloride (PDDA) polyelectrolyte, and finally by means of an electrostatic force, the negatively charged Fe3O4 magnetic nanoparticles formed a uniform dense covering layer on the graphene surface attached with PDDA layer, to obtain magnetic graphene. The magnetic graphene was aligned under the external magnetic field. The results showed that the graphene could be magnetized effectively by the polyelectrolyte layer-by-layer assembly technique. The alignment effect of powdery graphene was better than that of flaky graphene. The more the polyelectrolyte PSS and PDDA were added, the better the magnetic effect was, under the experimental conditions that took flaky graphene as raw material. By using the polyelectrolyte layer-by-layer assembly technique, the graphene can be magnetized effectively and aligned under the action of the magnetic field.