Organic fertilizer can improve soil management and alleviate soil nutrient loss caused by excessive fertilization. This study determines a fertilization scheme that can achieve high and stable crop yield and effective soil fertilization by exploring the effects of different organic fertilizer proportions on soil nutrient content, fertilizer utilization rate, and wheat yield. The experiment was conducted from 2018 to 2020 using the Xinchun 38 wheat variety and gray desert soil. The experiment used six treatments: no fertilizer (CK), with normal nitrogen and phosphorus fertilizer (CF). The amount of conventional chemical nitrogen fertilizer was reduced by 6%, 12%, 18%, and 24%, respectively, and supplemented with organic nitrogen fertilizer of the same proportion. The experimental treatment codes were SF6, SF12, SF18, and SF24, respectively. Plant samples from six wheat growth stages and 0–20 cm soil samples were collected to analyze the nitrogen and phosphorus content and organic matter; dry matter accumulation, crop yield, and yield components were measured at the harvest stage. Soil available nitrogen, phosphorus, potassium, and soil organic matter contents increased with the replacement ratio of organic fertilizer after three consecutive years of application. The available nutrients and organic matter in soil treated with SF18 and SF24 were significantly higher than those in CK and CF. The dry matter accumulation and nutrient accumulation of wheat increased with increasing organic fertilizer replacement rates of SF18 and SF24, respectively. Nitrogen and phosphorus fertilizer utilization rates, partial productivity, and agricultural use efficiency also increased, with the SF18 and SF24 treatments having higher organic fertilizer replacement rates than those in the other treatments. The number of ears, 1000-grain weight, and yield of wheat treated with SF18 treatment produced the best results. Therefore, continuously using organic fertilizer as a partial replacement for conventional fertilizer can increase wheat growth and soil nutrient availability, which can improve the utilization rate of fertilizer, thereby achieving stability and even a significant increase in yield.