To improve the quality of undergraduate education and implement the comprehensive and multi-dimensional education mode, we have taken the initiative of setting up a comprehensive design experiment of food microbiological detection module in our university since 2003. In this paper, the reform of practical teaching from the aspects of the course of opening the project, the key factors of project implementation, the primary focus of process education, the diversified quantitative assessment system, the feedback and reflection on teaching results were summarized. The practice results indicate that the module of food microbiology detection, as the feature and highlight of the course of microbiology experiment, had a good inheritance in the experimental preparation mode and scheme review mode. It plays an important role in cultivating students’ innovative spirit, scientific research quality, information quality, team spirit and data processing ability, etc. The special experiment mode is highly valued by teachers and students, which is unanimously recognized by peers. The establishment of diversified assessment system, such as process evaluation, promotes the teaching effect. The students have a higher evaluation on the experimental effect, who are satisfied with the learning results. In the next stage, this teaching mode can be further improved by strengthening the teaching team and cutting down learning burden of the students. The multi-dimensional and comprehensive talent training can be achieved in the modularization of food test experiment, which meets the current demand of “cultivating innovative, practical and comprehensive talents”, and therefore has a sound popularization value.