To explore the effects of different fertilization systems on carbon, nitrogen and phosphorus contents and ecological stoichiometric ratio of farmland soil and plant ecosystem in a long time can provide reference for revealing the energy balance and nutrient cycle of the system and realizing the balance and sustainable development of agricultural ecosystem elements. In this study, the long-term fertilization experiment at the Loess Plateau agricultural ecology experimental station of Changwu, located in the semi-arid region of the Loess Plateau, was taken as the research object. No fertilization (CK), single application of nitrogen (N), single application of phosphate (P), single application of nitrogen and phosphate (NP), single application of organic fertilizer (M), combined application of nitrogen and organic fertilizer (NM),application of phosphate and organic fertilizer(PM), and combined application of nitrogen and phosphate and organic fertillizer were selected. The contents of C, N and P in soil, microbe and plant in typical agricultural ecosystem of the Loess Plateau were analyzed, and the change rule of stoichiometry and its influencing factors were analyzed. The results showed that:(I) compared with CK, long-term single application of organic fertilizer and fertilizer combined with organic fertilizer treatment could significantly improve the carbon, nitrogen and phosphorus content of soil and organic matter. (II) With the input of exogenous nitrogen and phosphate fertilizer, compared with CK treatment, N and P treatment significantly reduced soil and wheat C:N and N:P, respectively, and P treatment significantly reduced organic matter and wheat C:P. However, the effect of organic fertilizer combination on microbial biomass and wheat C:N:P was more obvious. (III) There was a significant correlation between soil nutrients and the stoichiometric ratio of wheat under the condition of long-term organic fertilizer application, compared with no fertilization. The results showed that long-term fertilization significantly changed soil carbon, nitrogen and phosphorus contents and stoichiometric ratio, and fertilizer combined with organic fertilizer could significantly improve soil fertility in the xeroxic farmland of loess, resulting in the change of stoichiometric ratio of organic matter and microbial biomass, which had a significant impact on the stoichiometric ratio of wheat plants.