Innovating the labor education through specialized courses to improve the labor and thinking literacy of students is a new requirement for strengthening the labor education of college students in the new era. With consideration to the characteristics of the course Microbiology and the needs of student development, this paper expounded the importance of carrying out labor education in specialized courses and redefined the contents and objectives of labor education in the teaching of this course. Our team deeply explored the labor education resources contained in Microbiology based on the two major paths of cultivating Marxist labor value and improving labor literacy and creative ability, and adopted various teaching modes and methods to explore the labor education in the teaching of Microbiology. The practice showed that the reform had significantly enhanced students’ interest in learning, curiosity, and sense of professional identity, responsibility, and mission, and encouraged students to continuously strengthen their professional knowledge and skills. Moreover, students’ labor literacy, creative labor ability, and learning performance have also been significantly improved. The results suggest that the reform has achieved good labor education in the course teaching.