Combined with the characteristics of “problem setting” and “problem solving” of Problem-based learning (PBL) method, a novel teaching model suitable for the experimental courses was developed based on the theories of Flipped classroom. Taking the practical problem of “water is suspected of being contaminated by feces” as an example, the innovative teaching design and application was explored for the course of Environmental Biology Experiment, which is one of the basic courses for environment specialty undergraduate in higher education. The teaching model was carried out as followed: pre-class preparation, class implementation and after-class feedback. In the pre-class preparation process, the teaching team need to set up a number of related experimental scenarios for the practical problem, prepare the teaching resources such as teaching video, and arrange students to learn and complete the self-learning tasks. During the class, students were directed to perform experiment, observe and record the results, and were inducted to how to think by asking questions. After class, students were required to submit the experiment reports, to complete the consolidation exercises and feedback the problems. The practice showed that this PBL teaching model based on flipped classroom was successful and was worth promoting.