This study investigated how domain specificity of academic motivation related to the connection between instructional clarity and academic achievement in science and mathematics. It focused on three aspects of domain-specific academic motivation--self-concept, intrinsic value, and utility value--drawing from the Expectancy-Value Theory model. The study analyzed data from a nationally representative sample of 9060 eighth-grade students in Australia, with an average age of 14.1 years. After controlling for student demographics, socioeconomic status, and parental education level, the findings from structural equation modeling showed that instructional clarity positively related to students' mathematics achievement but did not significantly relate to their science achievement. Academic self-concept in both science and mathematics subjects was identified as the strongest motivational factor in student achievement. Additionally, the study demonstrated that instructional clarity was a stronger predictor of academic motivation to learn science compared to mathematics. These results offer empirical support for the connection between instructional clarity and students' academic achievement in science and mathematics via a domain-specific motivational pathway.