In order to explore the effective measures that could make rational fertilization and improve nutrient utilization of rice, 8 field experiments were conducted in the Yellow River irrigation region of Ningxia from 2016 to 2018 to evaluated the effect of side deep fertilization technology based on nutrient expert system(NE-SD) on rice yield and nutrient use efficiency. The results showed that, compared to the farmer practice fertilization (FP) treatment, the nutrient expert system (NE) treatment significantly reduced N and P application rate 24.85% and 24.78%, but increased K rate 90.71%, and increased the rice yield 4.71%. Compared to the FP treatment, the nutrient accumulation of nitrogen, phosphorus, and potassium increased 2.24%, 4.40% and 15.09%, respectively; the nutrient utilization efficiency of nitrogen, phosphorus, and potassium increased 9.84, 8.78 and 1.99, respectively; the fertilizer agronomic efficiency of nitrogen, phosphorus and potassium increased 4.73, 7.69 and 1.54 kg/kg, respectively. The side deep fertilization technology based on nutrient expert system could deepen the 4R nutrient management principle and had better application effect. Compared to the FP treatment, the rice yield of the NE-SD treatment increased 7.53%. Compared to the FP treatment, the nutrient accumulation of nitrogen, phosphorus, and potassium increased 3.92%, 7.87% and 18.74%, respectively; the nutrient utilization efficiency of nitrogen, phosphorus, and potassium increased 11.09, 11.32 and 5.82, respectively; the fertilizer agronomic efficiency of nitrogen, phosphorus, and potassium increased 5.87, 11.31 and 3.54 kg/kg, respectively. Therefore, on the basis of reducing fertilizer rate, two fertilization methods of the nutrient expert system and the side deep fertilization technology based on nutrient expert system could increase rice yield and nutrient accumulation, improve nutrient utilization efficiency, and reduce soil nitrogen and phosphorus surplus in Yellow River irrigation region of Ningxia.