The moral quality of students in agricultural and forestry colleges and universities in the new period has a positive mainstream tendency, but at the same time there are some unavoidable problems. The instrumentalization of traditional moral education mode, mechanical preaching and the characteristics of knowledge education are the important reasons for the emergence of problems. The agricultural and forestry colleges and universities must realize the transformation and innovation of moral education mode, reshape the main position of moral education of college students, rebuild the core value of moral education which pays close attention to the growth of individual life, and reconstruct the way of realization of moral education in colleges and universities.