Visual discomfort is an important factor in determining QoE in 3DTV. It can be measured by physiological signals. In this study, the relationship between 3D video characteristics (e.g., motion type, disparity, velocity, etc), visual discomfort and eye blinking rate were studied. Three motion types were considered, which were static scenes, planar motion and in-depth motion. 44 stimuli with different motion types, disparity levels and velocity levels were studied. The eye blinking signals of 28 observers were obtained by an electrophysiological measurement device. The experimental results showed that stimulus velocity affected eye blinks significantly and differently for planar motion stimuli and in-depth motion stimuli. The objective eye blinking model for 3D stimuli was developed in function of the 3D video characteristics. Furthermore, the results showed that eye blinking rate was proportional to the visual discomfort of the static 3D stimuli but inversely proportional to the visual discomfort of planar motion stimuli.