In this paper, the problem-based learning(PBL) method was applied in the teaching reform of finite element analysis course of engineering by taking the classical cantilever beam structure as a sample. The independent exploration spirit of students was encouraged, while the teacher was released from the heavy work of lecture and demonstration. In order to achieve the goal of knowledge integration, a series of research problems and open modeling approaches were presented and suggested in sequence, which helped to break the limits of knowledge between different chapters. The teaching program and evaluation criterion were also improved and modified according to the educational feature of graduate student. Practical teaching results indicated that the PBL method can be suitable for students with different learning abilities, which was beneficial to relieve the pressure of class hour distribution. The in-class communication and learning environment were also promoted in this way, which was in good accordance with the training requirement of scientific research capacity of graduate students.