The Nutrient Expert system (NE) has been proposed to improve yield and nitrogen (N) use efficiency (NUE) in the double rice cropping systems in China. However, the advantage of the NE system has yet to be quantified experimentally. A four-year field experiment was conducted in a double rice cropping system in China, to evaluate the ability of NE in improving yield and NUE. The experimental treatments consisted of NE based fertilization, current farmers’ practices (FP) and soil test based fertilizer recommendation (ST), and a series of nitrogen (N) rate treatments. The NUE decreased with increasing N application, while the yield did not increase significantly beyond N application rates of about 140 kg ha−1 (corresponding to the amount proposed by NE) in both early and late rice. NE increased grain yield (by 10.3% and 6.3%) and N uptake (by 5.7% and 4.0%) compared with FP and ST, respectively. NE significantly increased NUE compared with FP, and decreased the N surplus in comparison to FP and ST. The N dilution curve was Nc = 34.50 W−0.55 for early rice and Nc = 37.71 W−0.59 for late rice (where Nc is the N concentration in g kg−1, and W is the dry matter accumulation in t ha−1). The relationship between relative yield and the nitrogen nutrition index derived from the dilution curves confirmed that NE offered an optimum N application rate (approximately 140 kg ha−1) for both early and late rice. Carbon (C) and N translocation from vegetative organs to grains was enhanced with increasing N rate, while NE significantly increased C and N translocation compared with FP. Overall, the NE system ensured a high rice yield, increased N uptake and NUE. Therefore, the NE, as a user-friendly tool, is a sustainable fertilizer recommendation approach suitable for double rice cropping system, especially when soil testing is not available or timely for smallholders.