Abstract: Scientific and technological innovation is the core factor of industrial competitiveness and the first driving force to promote industrial upgrading. In the process of transformation and upgrading, regional characteristic industries cannot do without the power of scientific and technological innovation, and must rely on scientific and technological innovation to break through the constraints of resources and environment, expand development space, and improve the quality and efficiency of development. Based on the innovation theory and industrial structure theory, based on the influence mechanism of scientific and technological innovation on agricultural industry upgrading, this paper analyzed the limitations of scientific and technological innovation measures in planting technology, variety research and development and deep processing in the transformation and upgrading of Gannan navel orange, and put forward the countermeasures to promote the upgrading of Gannan navel orange industry from the theoretical level.