Abstract: Using factor analysis, scientific and technological innovation capacity of the agricultural scientific research institution of Inner Mongolia was carried out by quantitative analyzed, and it turned out that the keys to affect the innovation capacity were the input-output factor, achievement transformation factor, economic base factor and human input factor. We put forward related suggestions on promoting the technological innovation capacity of the agricultural science and technology from six aspects, included in enhancing input in agricultural innovation, strengthening agricultural scientific and technological talents development, intensifying protection of the intellectual rights, promoting agricultural sci-tech popularization, constructing scientific and technological information platform, and introducing enterprises to get involved in the scientific and technological innovation and promotion.