Practice has proved that agricultural science and technology is related to the supply capacity of agricultural goods, agricultural development, rural prosperity and rural incomes, and country’s long-term stability, and obviously, it is very important for China, a developing agricultural country. This paper has studied the influence of agricultural FDI on contribution rate of agricultural scientific and technological progress based on the panel data of 13 provincial administrative units from 2000 to 2012. The results show that under the premise of controlling other variables, the impact of agricultural FDI on agricultural science and technology contribution rate is significant. Except the indicator of rural financial scale, the pre-agricultural science and technology contribution rate, the inputs of researchers, the structure and efficiency of rural financial, the fixed asset investment in rural areas and rural human capital have a significant impact on the contribution rate of agricultural scientific and technological progress.