Microbial application technology is a professional foundation course with its typical feature of combining theory, practice, and application in aquaculture technology. Because of the existed problems in the course content, teaching mode, and evaluation method of the current teaching, this paper firstly selects the course content based on the professional positions requirements and vocational standards and reconstructs the teaching content based on the systematization of the work process, then adopts the online and offline mixed teaching mode with the digital resources jointly built by school, enterprise, profession, and industry, finally applies the four-dimensional binary evaluation method to evaluate the learning effect. Practice teaching shows the course developed in this paper can effectively stimulate students’ learning enthusiasm and significantly improve teaching quality and teaching effect.