A number of prominent educators have confirmed that developing learners’ metacognitive strategies about listening is an important way of helping them learn how to listen to improve their listening. With the rapid development of information and communication technologies, many listening training systems provide various types of help options in support of listening comprehension. However, learners may be unaware of how effectively use these help options or they may rely too heavily on them, thus reducing the effectiveness of their listening practice. Therefore, this study develops a digital pen-based learning system with a reward mechanism that guides learners through the metacognitive processes effectively use available help options to develop listening skills. Two experiments were performed to evaluate the effects of the proposed system on learners’ listening achievement, motivation, and metacognitive awareness. The experimental results indicated that the proposed system improved learners’ listening comprehension, learning motivation, and metacognitive awareness. A lag-sequential analysis was conducted to infer learners’ behavioral patterns to explore how learners used the help options to perform listening tasks. Several interesting behavioral patterns were found and discussed.