The agricultural science and technology innovation efficiency and its’ changes in 3 grain functional areas in China from 2001 to 2019 are measured and compared by using the Super-efficiency DEA model and the Malmquist index method from the perspective of grain functional areas. The results show that the efficiency in different grain functional areas shows a fluctuating upward trend during the period of 2001 to 2019. The agricultural science and technology innovation efficiency among 3 grain functional areas from low to high in turn are main grain production area, grain production and selling balance area and main grain selling area. The main grain production area has scale efficiency advantage, main grain selling area has technology progress advantage, and balance area’s efficiency fluctuation range is highest. Finally, suggestions are given from the perspective of overall planning and optimizing the allocation of agricultural science and technology innovation resources in each grain functional area, and reasonably promoting the agricultural science and technology innovation and its efficiency in each functional area.