It is very important to train practical ability of the students in logistics engineering. In the traditional practice teaching, often only pay attention to the software operation of the laboratory and neglect the practical training that combines with the actual enterprises in order to help the enterprises solve their practical problems. This will lead to the disconnection between the students and the reality, which prevents the students from applying the theory and expertise they has learned. To cultivate innovative talents in logistics, students need to integrate more practical problems, and theoretically and practically analyze and solve them. In this paper, we design the teaching of logistics system planning and simulation practice in the logistics system planning and simulation course. We proposed how to analyze and design the production logistics system in combination with actual cases, and simulate the actual system. Through the case design, it can improve the students’ ability to solve the practical problems in combination with actual case. This design can provide the instructors the practical case of the related course, and also give references for how to improve the practical and innovative ability of logistics engineering students.