The invention provides a method for predicting county-scale leaching total nitrogen discharge caused by farmland non-point source pollution. The method comprises steps as follows: 1) determining farmland non-point source pollution leaching total nitrogen generation subareas and county administrative division ranges; 2) selecting factors affecting leaching total nitrogen discharge; 3) acquiring leaching total nitrogen discharge in the N year as well as the quantity of factors affecting leaching total nitrogen in the N year and (N-x) year on the basis of biochemical detection of county-scale areas; 4) establishing a prediction model about the factors affecting the leaching total nitrogen in the N year and the (N-x) year; 5) substituting numerical values obtained in Step 2) into a mathematical model to obtain the leaching total nitrogen discharge in the (N+x) year. The method aims to solve the problem that county-scale leaching total nitrogen caused by farmland non-point source pollution cannot be predicted, on the basis of farmland non-point source pollution division, the prediction model about the leaching total nitrogen discharge is established, the farmland leaching total nitrogen discharge is predicted, and technical support is provided for control on farmland non-point source pollution.