Better understanding of soil fertility and nutrient balance in soil-crop systems is important for rational fertilization, refining agricultural management practices and improving utilization efficiency of water, soil and fertilizer resources. Traditional statistics, geostatistics combined with GIS technology were used to evaluate the spatial and temporal variability of soil organic matter (OM), available nitrogen (AN), available phosphorus (AP) and available potassium (AK) in Weibei rainfed highland from the 1980s to 2010—2012 based on the data from the second national soil survey and the cultivated land productivity investigation and quality evaluation project. Meanwhile, the current situation of fertilization and nutrient balance in main cropping systems was analyzed based on the information from household surveys of the national soil testing and fertilizer recommendation project during 2010 to 2012. The results indicated that the current average contents of OM, AN, AP and AK in soil were 12.9g/kg, 59.4mg/kg, 15.4mg/kg and 164.2mg/kg, respectively. Compared with 1980s, the OM, AN and AP contents in soil have been increased by 22.0%, 37.9% and 129.8%, respectively, and AK was kept stable. Compared with the rational fertilizer application rates, the ratios of households using excessive nitrogen (N) inputs in wheat, maize and apple were 89%, 69% and 74%, and the ratios for phosphorus (P) were 75%, 49% and 52%, respectively. The ratios of households using insufficient potassium (K) inputs in wheat and maize were much higher, which were 76% and 67%, respectively. Meanwhile, the ratios of households using excessive and insufficient K inputs in apple were 40% and 48%, respectively. Significant surpluses of N and P in wheat, maize and apple cropping systems were observed, with an average of 116, 111 and 655kg/hm2 for N, 88, 56 and 357kg/hm2 for P, respectively. N and P practical surplus rates were much higher than their permissible surplus rates, indicating that N and P surpluses in this area were greatly exceeded their rational ranges. K was in deficit in wheat and maize cropping systems, with an average deficit of 73 and 93kg/hm2, respectively, which were both within their permissible scopes. K was in surplus in apple cropping system, with an average of 283kg/hm2, which was 145 percentage points higher than its permissible surplus rate. From the perspective of food safety and environmental protection, inputs of N and P in this area should be reduced. By contrast, input of K should be increased to maintain high and stable cereal crop yields.