Firstly, the related theories about agricultural science and technology innovation and project approval evaluation are combed and summarized. By combining application and finish books of science and technology support plan project in agricultural field of Ministry of Science and Technology with stronger innovation, case analysis and expert interview are conducted. Evaluation indexes of agricultural science and technology project based on innovation value are proposed initially, and there are 50 initial indexes. After that, via focus group talk, qualitative research is conducted to further adjust innovative evaluation indexes, and 50 initial indexes are deleted to 41. The importance of the 41 indexes is scored by the experts, and index screening and classification are conducted by verification factor analysis in structural equation model. It not only obtains index classification but also finds action mechanism among innovation demand, innovation mode, research thinking, treatment method of difficulty, and predicted risk. The research could straighten up ideas of project review experts in agricultural field and provide reference for applicant designing project.