Recent research in collaborative learning has indicated that peer assessment has a positive influence on students' learning performance and learning process. This study investigates how the different subgroups of two roles (assessors and assessees) in peer assessment contribute to students' perceptions of science learning in mobile technology-supported collaborative learning (MSCL), including learning motivation, self-efficacy, group efficacy, and anxiety level. In total, 128 fifth-grade students participated in this study. They were asked to complete science inquiry tasks in groups with the support of mobile devices throughout a semester and to conduct a peer assessment activity at the end of the semester. According to scores from others and scores to others in peer assessment activities, we divided the students into subgroups (high, medium, low). The results indicate that the self-efficacy and group efficacy of students in the high score group were significantly higher than that of the medium score group when they act as assessors. Moreover, as assessees, the learning motivation of the high score students was significantly higher than that of the low score students, and the anxiety level of the low score students was significantly higher than that of the medium score students. These findings have important implications for the design of peer assessment activities and may help teachers identify the potential usages of peer assessment to enhance students' positive perceptions in MSCL.