Visual fatigue of 3D display restricts its wide application, moreover, human attention is one of important factors for visual fatigue due to the fact that perceptual salient regions determine the quality of experience of 3D contents. In order to study the relationship between 3D image salient area and 3D visual fatigue, an experiment is designed in which subjects are required to accomplish a task realized with 3D display system, eye tracking system and ECG detecting apparatuses. The aim of the task is to induce 3D visual fatigue with stimuli with different salient areas. ECG signals and eye tracking parameters are recorded during the whole process and the questionnaire is adopted to obtain the subjective fatigue parameters. Analysis of the experimental data shows the relationship between salient area and visual fatigue. In our research, an evaluation method of visual fatigue by considering both ECG signals and eye tracking parameters is developed, and a visual fatigue evaluation model based on salient area of 3D images is introduced. In our future study, more elements will be added into the experiment to find more factors which can induce 3D visual fatigue.