The invention discloses a carbon-based metal phosphide loaded catalyst, a preparation method and application thereof. The preparation process of the carbon-based metal phosphide loaded catalyst includes: mixing a precious metal salt, deionized water and a phosphorus source evenly, then adding a nitrogen-containing organic matter and stirring the substances evenly, transferring the obtained solution into a polytetrafluoroethylene tank, carrying out hydrothermal reaction at 120-180DEG C for 10-24h, at the end of the reaction, conducting cooling to room temperature, filtering the reaction liquid,drying the filter residue, then placing the filter residue in a tubular furnace, in nitrogen atmosphere, raising the temperature from room temperature to 700-900DEG C at a rate of 3-8DEG C / min, thenkeeping a constant temperature for 1-4h, then performing natural cooling to room temperature, cleaning the calcinations product with deionized water and anhydrous ethanol respectively 3-5 times, performing pumping filtering, and drying the filter residue, thus obtaining the carbon-based metal phosphide loaded catalyst. The carbon-based metal phosphide loaded catalyst prepared according to the invention is low in cost, and has high catalytic activity and stability in the electrocatalytic hydrogenation reaction of lignin phenol compounds.