The Agricultural Resources and Environment major was taken as an example to explore the reform of practical innovation and entrepreneurship teaching system under the guidance of new agricultural science education. The necessity of reforming the teaching system was analyzed, the areas for improvement in the teaching system were explored, and the requirements of the new agricultural education orientation for the reform of the teaching system were proposed. Starting from the construction of innovative curriculum system, optimization of talent training model, and construction of teaching resources and teaching staff, the ways of teaching system reform were analyzed. These reform measures, it was beneficial to promote the practical innovation and entrepreneurship teaching system of Agricultural Resources and Environment major to be more in line with the new agricultural science education orientation, comprehensively cultivate and exercise students’ practical abilities, and make them better adapt to the requirements of modern agricultural development.