Abstract: The lower fertilizer using efficiency of grain production is a main obstacle to improve grain yield. It not only pushes production cost rising, but also causes seriously agriculture non-point source pollution. In this paper, using stochastic frontier production function, we calculate production technical efficiency and fertilizer using efficiency of wheat, corn and rice in major grain provinces of China from 2006 to 2009. Moreover, we analyze the factors which affect fertilizer using efficiency. The result shows that average fertilizer using efficiencies of wheat, corn and rice are 0.37, 0.26 and 0.37. Education level, income level, fertilizer prices, financial support for agriculture and scale of planting are important factors to determining fertilizer using efficiency.