Quality education for college students imposes certain requirements in the 21st century. They should not only have a good command of theoretical knowledge but also with greater attachment on cultivating scientific thinking and inspiring innovation. In order to cultivate their ability on innovation and promote quality education, a teaching mode of “theoretical courses+innovative project design” were explored in microbiology. In the process, some practices, including the course content adjustment, case introduction, and evaluation system were implemented. The results showed that this mode exert significant influence on the knowledge grasping and expanding, scientific thinking cultivation, along with innovation stimulation. This exploration also roles as a strong boost for quality education in colleges and universities.