Abstract: As one of the important steps, analysis of crop yield-limiting factors plays an important role in variable-rate fertilization of precision agriculture. The results based on decision-making tree and GIS overlay analysis show that the soil organic matter always holds the first place in all knowledge rules, P and N rank the second. It is obvious that the yield spatial distribution with organic matter, N and P have high superposition, and the superposition rates are 91%, 83% and 49%, respectively. The experiments on Nuanquan Farm, Ningxia Hui Autonomous Region also display that soil organic matter, P and N are the main yield limiting factors for wheat in this area, thus increasing soil organic matter would be an important measure for increasing wheat yield. It is believable that the method of analysis yield-limiting factors based on the decision-making tree and GIS overlay is practical in similar areas like Ningxia according to the theoretical research and its application.