The invention discloses a fertilizing method in relay intercropping planting of potatoes and soybeans. The fertilizing method is based on a principle that leguminosae and nodule bacteria can form root nodules to immobilize nitrogen in atmosphere so that addition quantity of a chemical nitrogen fertilizer is reduced. The fertilizing method aims to the nutrient characters that topsoil in Northwest region is low in carbon (organic substances), is lack in nitrogen and phosphorus and is rich in potassium. On the basis of recommended nitrogen application quantity in soil testing formula, the nitrogen fertilizer is applied with the quantity reduced by 30%, wherein the ratio of immobilized nitrogen (N) to phosphorus (P2O5) to potassium (K2O) is 1:1:0.5. The fertilizing method employs a base fertilizer including 50% of a nitrogen fertilizer, 100% of a phosphorus fertilizer, 70% of a potassium fertilizer and 100% of an organic fertilizer and a topdressing including 50% of the nitrogen fertilizer and 30% of the potassium fertilizer. The fertilizing method provides technical guarantee to achievement of a three-win situation comprising yield increasing of crop, improvement of soil fertility and environment-friendly fertilization under a potato-soybean relay intercropping mode in Northwest region. The fertilizing method has following beneficial effects: (1) the method promotes yield increasing of both potatoes and soybeans and increases economic benefit; (2) the method improves soil situation and soil fertility; (3) the method increases utilization rate of the fertilizers and reduces environment pollution; and (4) the method can regulate nutrients and prevents and treats diseases and pests in crop.