According to Eye-Mind theory, eye movement has been considered an indicator of attention and thinking. The objective of this research is to explore the difference of prior knowledge on eye moment while participant understanding in scientific diagrams by Plate tectonics for example. Thirty-six participants were voluntary university students who majored in science. A drawing test was conducted to the participants as well as an eye tracking test was conducted while participant understanding scientific diagrams, At last, Retrospective Think Aloud was used to realize prior knowledge of participants and the progress after understanding scientific diagrams. The data showed that (a) Higher prior knowledge group paid more attention on textual representation rather than Lower prior knowledge group, and more tended to get information of diagrams through textual representation. (b) Higher prior knowledge group had an attempt on understanding scientific diagrams through mapping textual representation and textual representation, textual representation and Plate tectonics diagrams. (c) The participant obtained sufficient information to adjust Plate tectonics concepts by himself or not was related to fixation position.