In eye-tracking based 3D displays, system latency due to eye-tracking and 3D rendering causes an error between the actual eye position and the tracked position, which is proportional to the viewer’s movement. This discrepancy makes viewers to see 3D content from a non-optimal position, thereby increasing 3D crosstalk and degrading the quality of 3D images under dynamic viewing conditions. In this paper, we investigate the latency issue, distinguish each source of system latency and study the display margin of eye-tracking based 3D display. To reduce 3D crosstalk during viewer’s motion, we propose a motion compensation method by predicting viewer’s eye position. The effectiveness of our motion compensation method is validated by experiments using previously implemented 3D display prototype and the results show that the prediction error decreased to 24.6%, indicating that the accuracy of eye pupil position became 4 times higher, and crosstalk reduced to a level similar to that of a 1/4 latency system.