Based on the survey data of farmers in the Yangtze River economic belt provinces including Yunnan, Hubei and Jiangsu, this paper adopts the Tran-slog stochastic frontier production function to measure the fertilizer application efficiency and then uses the Tobit model to estimate the impact of adopting soil testing and formulated fertilization technology on fertilizer application efficiency in rice production. The research results show that: (1) The fertilizer application efficiency of rice farmers in the Yangtze River Economic Belt can be improved 31.5% potentially; the fertilizer application efficiency in the upper reaches (Yunnan) is relatively lower than the middle (Hubei) and the lower reaches (Jiangsu) of the Yangtze River. (2) The fertilizer application efficiency of rice is lower than the technical efficiency in the Yangtze River Economic Zone, indicating that reducing fertilizer use would not lead to the decline of rice yield and would contribute to the improvement of fertilizer application efficiency. (3) Adopting soil testing and formulated fertilization technology can significantly improve fertilizer application efficiency, but for farmers who originally have higher fertilizer application efficiency, the effect of adopting soil testing and formulated fertilization technology on improving fertilizer application efficiency has been proved to be lower. (4) Further analyses indicate that the well-facilitated capital farmland construction project increases the joint planting scale and thus improves the positive effects of adopting soil testing and formulated fertilization technology on fertilizer application efficiency.