The invention belongs to the field of energy material preparation and application, and discloses a nitrogen-doped carbon-coated nanoflower-shaped MoSe2 composite material and preparation and application. The method comprises the following steps: 1) adding selenium powder into a sodium borohydride solution, mixing, adding a molybdenum source solution, stirring and mixing, further adding an organic carbon source, putting into a high-pressure reaction kettle, performing a heat-preservation reaction, cooling, filtering, washing, drying, and calcining in an inert gas atmosphere, so as to obtain a MoSe2/C product; 2) dispersing the MoSe2/C product into water, adding a nitrogen source, performing ultrasonic treatment, performing heating stirring till being evaporated to dryness so as to obtain a precursor; (3) heating the precursor in the inert gas atmosphere, and calcining at 500-700 DEG C, thereby obtaining the nitrogen-doped carbon-coated nanoflower-shaped MoSe2 composite material. The nitrogen-doped carbon-coated nanoflower-shaped MoSe2 composite material is relatively large in specific surface area, good in hydrogen separation catalysis activity and stability, simple in method, wide in raw material source, low in cost and applicable to large-scale production.