Abstract: Based on the analysis of the rich connotation of scientific and technological innovation in China under the new situation, the new management tasks, new management modes and new management responsibilities faced in the scientific research management of agricultural research institutions under the background of scientific and technological innovation were discussed in this paper, and then some innovative suggestions on the scientific research management of agricultural research institutions under the new situation were put forward from the following aspects including the guidance of party construction, the implementation of document spirit, the strengthening of supervision and management, the strengthening of scientific research integrity, the promotion of international exchanges and cooperation, and the acceleration of functional transformation, etc.