The purpose of this study is to examine students' perceptions of instructional practices in the classroom, and to further investigate the relationships among instructional practices, motivational beliefs and science achievement. Hierarchical linear modelling was utilised to examine the Trends in International Mathematics and Science Study 2007 Taiwanese eighth grade student data. The results indicated that the students perceived a greater frequency of teacher-oriented instructional practices applied in the classroom than student-oriented practices. Moreover, teacher-oriented instructional practices have a positively significant relationship with student science achievement, while student-oriented instructional practices do not show such a relationship. The results also show that teacher-oriented instructional practices positively moderate the relationship between students' self-concept and achievement, but negatively moderate the relationship between intrinsic interest and achievement. On the other hand, the student-oriented instructional practices show the opposite pattern of moderating the relations between motivational beliefs and achievement while they are not statistically significant. The study sheds light on the dynamic relationships between students' motivational beliefs and science achievement changes as a function of instructional practices.