Optimizing the allocation of agricultural science and technology resources is an important condition for achieving high-level agricultural science and technology self-reliance and building an agricultural power, and the provincial Academy of Agricultural Sciences, as an important part of agricultural science and technology innovation, must make efficient use of limited scientific and technological resources. According to the theory of resource misallocation, a model of misallocation of scientific and technological resources was constructed, and the relative mismatch index of scientific and technological human resources and scientific and technological financial resources and the loss of scientific and technological output in 26 provincial agricultural academies in China from 2005 to 2019 were measured, and the pulling effect of scientific and technological human resources and scientific and technological financial resources was compared with scientific and technological output. The results show that the degree of relative mismatch of scientific and technological resources of agricultural academies in different regions and provinces is different, among which the misallocation of scientific and technological resources in North China and Southwest China is more serious. The misallocation of scientific and technological resources leads to the loss of about 10% of scientific and technological output, and the misallocation of scientific and technological human resources is the main reason for the loss of scientific and technological output; The mismatch of scientific and technological financial resources and the pulling effect of scientific and technological output are more obvious. On this basis, policy suggestions are put forward to improve the misallocation of scientific and technological resources of the Academy of Agricultural Sciences in order to enhance the ability of scientific and technological innovation.