This study was designed to find out an optimised planting system of reducing non-point (source) pollution by analyzing the reasons and the factors of influence non-point pollution in farmland of Erhai Lake basin. The results showed that incomes, residual nitrogen in soil, and the loss of nitrogen in surface water in rice-garlic system were higher than those in rice-fava bean system. There were positive correlations between the nitrogen loss of farmland, nitrogen inputs, residual nitrogen in soil, and incomes of farmland. Economic benefits and environment benefits are both appropriate, if the area of rice-garlic system would be reduced to 53% and the area of rice-fava bean system increased to 36% of total cropping area in the investigated watershed. Adjustment of planting structure and introduction of reasonable rotation systems is considered an effective measure of controlling agricultural non-point pollution in watersheds of Erhai Lake.