This study used eye-movement tracking to investigate how students engage with the learning process of reading science articles with or without hands-on manipulation of a pulley system and their influences on learning outcomes. This experiment used a 2 (reading easy or difficult articles) × 2 (with or without hands-on manipulation) between-subject design. Seventy-nine undergraduate students participated. They first read a science article about rotational mechanics and then completed a problem-solving task. While completing the problem-solving task, the two pure reading groups could reread the article to write down their answers, and the two read-and-manipulation groups were allowed to manipulate the pulley system in addition to reading the article. The participants' eye movements were recorded during the completion of this task. Results showed that hands-on manipulation benefited those learners who read the difficult article, since they had better scores regarding the problem-solving task; this was not the case for those who read the easy article. Eye movement data showed that the two pure reading groups spent more processing time rereading the article as well as writing their answers to the problem-solving task than did the other two read-and-manipulation groups. Furthermore, the easy-article group spent significantly longer processing time on performing the experiment but not on preparing or planning for manipulating the pulley system than did the difficult-article group. The transition proportion of eye fixations reflected the looking and acting order of the participants during the problem-solving task and indicated groups' similarities (e.g., seldom did students refer to the article to manipulate the pulley system and in reverse) and differences (e.g., the difficult-article group preferred to check back-and-forth if their manipulation resolved the testing questions, but the easy-article group did so relatively seldom).