Taiwanese students are featured as having high academic achievement but low motivational beliefs according to the serial results of the Trends in Mathematics and Science Study (TIMSS). Moreover, given that the role of context has become more important in the development of academic motivation theory, this study aimed to examine the relationship between motivational beliefs and science achievement at both the student and school levels. Based on the Expectancy-Value Theory, the three motivational beliefs, namely self-concept, intrinsic value, and utility value, were the focuses of this study. The two-level hierarchical linear model was used to analyse the Taiwanese TIMSS 2011 eighth-grade student data. The results indicated that each motivational belief had a positive predictive effect on science achievement. Additionally, a positive school contextual effect of self-concept on science achievement was identified. Furthermore, school-mean utility value had a negative moderating effect on the relationship between utility value and science achievement. In conclusion, this study sheds light on the functioning of motivational beliefs in science learning among Taiwanese adolescents with consideration of the school motivational contexts.