Starting from the practical significance of the practice teaching reform of environmental microbiology under the background of New Engineering, this paper expounds the construction of the practice teaching mode of Environmental Microbiology course based on the requirements of New Engineering. The practical teaching mode is designed from four aspects: basic experiment of subject, cooperative training between school and enterprise, practice of curriculum design and moral education of teaching practice. The aim of the practical teaching mode is to improve students’ ideological and moral quality and practical ability so as to meet the needs of the development of environmental microbiology industry. Practice teaching effectively strengthens the interaction between teachers and students, stimulates students’ enthusiasm for practice and innovation, and provides a good practice platform for training compound and practical engineers who meet the requirements of New Engineering.