In order to understand spatial variability characteristics of soil nitrogen and phosphorus contents in the typical landscape units in Chaihe catchment, 72 surface soil samples were collected from the lands different in landscape and land-use types in Chaihe catchment. The contents of nitrogen, phosphorus, and organic matter of the soils were analyzed. Results showed that the soils in phosphorus mining area and forests of phosphorus-enriched area contained the higher phosphorus. The average contents of total phosphorus and available phosphorus were 20 g/kg and 3 687.7 mg/kg, respectively. The soils in sediments of ditches and Chaihe River contained the higher nitrogen. The average contents of total nitrogen and available nitrogen reached 2.99 g/kg and 631.8 mg/kg, respectively. The great variation of the contents of soil nitrogen and phosphorus were found in different land-use types in phosphorus mining area, slope farmland, and flatland. The results of nested ANOVA analysis of soil nutrient contents suggested that landscape, land-use and land spatial location co-determine the variability of soil nitrogen, phosphorus and organic matter contents in the catchment. It is, therefore, necessary to combine landscape with land-use and land spatial location together in risk assessment and control of non-point source pollution in Chaihe catchment.