The invention discloses an automatic efficient purification system for total nitrogen of water and a method of the automatic efficient purification system. The system comprises a purification system (1), a modification system (2), a total nitrogen detection system (3) and a denitrification system (4), wherein the purification system (1), the total nitrogen detection system (3) and the denitrification system (4) are sequentially connected, and the modification system (2) is connected to the purification system (1); the purification system (1) is used for supplying oxygen to microbes on a biochar matrix by using plant root system action and improving nitrification. The modification system (2) is used for carrying out aeration modification on the biochar matrix (1-2) through an aeration pump(2-1), so as to improve the microbial activity of the biochar matrix (1-2). The total nitrogen detection system (3) is used for monitoring total nitrogen in water, and the denitrification system (4) is started up to perform refluxing when the total nitrogen exceeds a set standard value, so as to improve hydraulic conditions and improve a denitrification effect. The system and the method are high in denitrification efficiency, good in treatment effect, small in investment and low in operating cost, biochar is subjected to resource-converting utilization, and in-situ purification does not need afloor area.