Objectives The integration point and the reforming measures for elements of value education in the course were studied to effectively promote the teaching reform of value education in the course of Aquatic Animal Microbiology in colleges and universities. Methods The teaching reform of value education courses in colleges and universities was improved and the value education was effectively integrated into the whole process of constructing the teaching in classroom by designing elements of value education in the course of Aquatic Animal Microbiology and reforming methods of teaching in value education. Results The level of value education among teachers in in colleges and universities was improved by designing elements of value education in the course of Aquatic Animal Microbiology. The syllabus of course and plans of teaching were revised. The teaching mode and methods of course were updated. The resources of value education in the course were mined. The assessment and evaluation of value education in the course was strengthened. The efficiency of teaching and the comprehensive quality of students was improved, achieving the goal of collaborative education between professional courses and value education courses. Conclusions Teachers in colleges and universities can comprehensively improve the theoretical knowledge and practical skills of students, collaborate to cultivate professionals with high-quality and high-level in aquaculture, promote the integration of industry- colleges and universities -research by continuously exploring and reforming the methods of teaching combined with the requirements of value education in courses. It will provide strong support for value education in the course of Aquatic Animal Microbiology, and lay a solid foundation for the sustainable development of the aquaculture industry.