Microbial Engineering is a practical and applied course, it is therefore an indispensable part of teaching to let the students practice in the production line of an enterprise. However, lack of internship resources has always been a bottleneck hampering the high-level internship training during teaching the Microbial Engineering course. A virtual production line developed based on information technology enables students to learn the theoretical knowledge of the complex production system. Moreover, it enables students to perform complex virtual operations, thereby improving students’ practicing and innovation abilities. In order to let the virtual simulation experiments project play a great role in undergraduate teaching, this article summarizes the progress, characteristics, and value of the virtual simulation experiments for Microbial Engineering. In addition, the main challenges that limit its shared application are also discussed, with potential solutions prospected.