The invention relates to a device for removing nitrate nitrogen in water and an application method of the device. The device is used for solving such problems of existing method for removing nitrate nitrogen in water as low electrochemical denitrification current efficiency, poor selectivity of a reaction product and need of the addition of H2 during catalytic hydrogenation and comprises a direct current power supply, a pH meter, a micro-peristaltic pump, a microfiltration membrane assembly, a water inlet pump, a first circulating pump, a water outlet pump, a cathode chamber, a cathode plate, an anode plate, an anode chamber, a second circulating pump and a proton exchange membrane. The method comprise the following steps: adding the polluted water body into the cathode chamber, adding a catalyst into the cathode chamber, switching on the direct current power supply, enabling nitrate ions adsorbed on the cathode plate to accept electrons and be gradually reduced to N2; enabling generated H2 to be gathered from the cathode plate into microbubbles, diffuse and be adsorbed on the catalyst, in the presence of the catalyst and reducing the residual NO3<-> into N2 with H2 as an electron donor and discharging into the air. The device is used for removing nitrate nitrogen in water.