The invention discloses a preparation method of a novel three-dimensional nitrogen doped graphene composite material system. The method comprises the following steps: 1, uniformly dispersing graphene oxide in a solvent at room temperature, adding a selected material and a nitrogen-containing compound, and uniformly mixing to form a mixed solution; 2, reacting the mixed solution at a temperature from room temperature to 150DEG C for 0-8h; and 3, cooling the above obtained product to room temperature, centrifuging, collecting the obtained product, washing, and drying to obtain the nitrogen doped graphene composite material. The three-dimensional nitrogen doped graphene composite material system with the nitrogen content of 8-19% can be efficiently and controllably prepared through the method, and the nitrogen content of the system can be controlled by changing the kind and the amount of the added nitrogen-containing compound, the reaction temperature and the reaction time; and the method is simple, is easy to enforce, allows the yield to be greater than 98.9%, and can be widely used in fields of water treatment, biomedicines, energy generation, conversion and storage devices, electrostatic prevention, heat management, heat conduction and dissipation, sensors, electromagnetic shielding, wave absorption and catalysis.