This study aimed to explore low and non-low achievers' motivation towards science learning among 8th graders in two public schools in central Taiwan under inquiry-based instruction. Mixed design research methods were adopted, and students were divided into experimental (n = 56) and control groups (n = 45). Six non-consecutive inquiry units (90--180 minutes each) were taught to the experimental group during one semester, while same topic units were instructed traditionally in the control group. A questionnaire measuring students' motivation towards science learning [MILS] was implemented as pre- and post-tests in both the experimental and control groups. Moreover, the teachers and 12 non-low achievers, and six low achievers from each group were interviewed four times in this semester. ANCOVA were used to analyze quantitative data in the questionnaire, and the interview data were coded. The results showed that statistically non-low achievers' achievement goals and perception of their learning environment in the experimental group significantly improved more than those in the control group. Practically, non-low achievers' expectancy and learning strategies and low achievers' confidence, value of science learning, achievement goals, learning strategies, and perception of learning environment in the experimental group were better than those in the control group. Low achievers still needed to use more learning strategies. Additionally, in the experimental group, hands-on activities and conceptual understanding motivated both achievers, various learning strategies motivated non-low achievers, and teachers and peers' assistance motivated low achievers. However, both achievers under intervention had more exam anxiety than those under traditional teaching due to their weak ability to calculate.