The study on input-output budget and fertilizer use efficiency of P and K nutrients was conducted in a 24-year long-term field located in Hexi Corridor by the nutrient difference method. The results showed that P nutrient input was always greater than output, which was the positive budget. The average surplus rate of chemical P fertilizers continuously applied as NP and NPK was from 43.3% to 97.0%. The total P average utilization rate of wheat and corn was 37.3%—40.5% and 22.3%—30.5%, respectively, the short-term P use efficiency increased by 12.8%—22.9% and 5.9%—9.5%. The average surplus rate of combining application of organic manure and chemical fertilizers (MNP, MNPK) was 211.3%—277.9%. The total P use efficiency of wheat and maize was 18.0%—18.3% and 16.3%—19.4% respectively, which increased by 5.4%—8.5% and 5.8%—6.6% higher than the initial test. The measures of continuous organic fertilizer application and moderate reduction chemical fertilizers were rational balanced fertilization method. The input of K was always lower than the output of crop uptake, it was the negative balance of K. Long-term application of organic fertilizers (MN、MNP) could not balance soil K, the average deficit was -38.6%— -47.2%. The total use of K in manure and the fertilizer rate of wheat and corn crops were 57.8%—59.8% and 34.1%—54.1% respectively, compared with initial trials which increased 8.4%—22.3%. K fertilizer average deficit was -36.2%— -67.8% by continuous chemical K application. K fertilizer use efficiency of wheat and maize was 53.1% and 29.5% respectively, which increased by 7.4%—36.4% than initial trials. It was the necessary measures to increase chemical fertilizers application on the basis of organic manure.