This study focuses on "high achievement but low motivation" phenomenon that is prevalent in East Asian countries and districts, and uses eighth graders in Taipei that participated in TIMSS 2007 as an example to examine the direct and indirect effects of academic motivation, positive affect, and instruction on science achievement. Confirmatory Factor Analysis and Structural Equation Modeling were employed to test measurement and structural models and indicated a good fit of the models to the data. The results showed that expectancy and value in science and inquiry-based instruction are three significant and positive predictors of students' positive affect toward science. In addition, expectancy, positive affect, and three types of instruction all significantly predicted students' science achievement after the number of books at home and mother's education were controlled. However, inquiry-based and practice-based instructions were negative predictors whereas traditional instruction was positive. The suppression role of the positive affect was partially supported between academic motivation and science achievement.