With the rapid development of the human computer interaction technology, the requirements on immersive 3D displays have increased greatly. However visual fatigue has become the bottleneck of the technology development of 3D display, it’s necessary to investigate the objective evaluation parameters of the visual fatigue and to find out the main factors that affect the visual fatigue in the 3D contents. The purpose of this paper is to study the relationship among the blinking rate, the motion characteristics and the visual fatigue when watching 3D videos. 20 subjects participate in the evaluation experiment and the blinking data are achieved from the output of an SMI eye tracker. The stimuli are different on the motion type, velocity and disparity. N-way ANOVA test and multiple comparison test are adopted to analyze the experimental data and the analysis results show that the linear relationships have been found between the subjective scores and the blinking rates, but the correlation coefficient is lower than that in the previous study. The results will be helpful for further research, and the different blink mechanisms of 3D motion types can be studied at the same time.