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Prior research demonstrated the effectiveness of direct-manipulation animation (DMA) as a congruent medium to support learners to understand dynamic systems and processes. However, the transient nature of animation poses cognitive load to learners, especially novices. Critical features of target concepts may not be seen or examined. Using eye-tracking technique, this study examined how learning instruction (explicit vs general) and spatial ability affect learners’ exploration of interactive animation to understand dynamic systems. Analyses of their eye-gaze patterns and learning performance revealed positive correlation between features inspected and quality of inferential reasoning. Findings suggest simple scaffold engenders mindful exploration which in turn promotes effective learning and robust reasoning. Spatial ability, however, was not significant in predicting interactive behaviors.