Focused on the issue that the traditional interest area based visualization method can not pay attention to the details in the process of analyzing pilot eye movement data, a visual analysis method of eye movement data based on user-defined interest area was proposed. Firstly, according to the specific analysis task, the self-divison and self-definition of the background image of the task were introduced. Then, multiple auxiliary views and interactive approaches were combined, and an eye movement data visual analysis system for pilot training was designed and implemented to help analysts analyze the difference of eye movement between different pilots. Finally, through case analysis, the effectiveness of the visual analysis method and the practicability of the analysis system were proved. The experimental results show that compared with the traditional method, in the proposed method, the analysts' initiative in the analysis process is increased. The analysts are allowed to explore the local details of the task background in both global and local aspects, making the analysts' analyze the data in multi-angle; the analysts are allowed find the flight students' cognitive difficulties in the training process as a whole, so as to develop more targeted and more effective training courses.