Although the relationship between the classroom learning environment and academic achievement has been explored in subject-free and disciplinary subject contexts, research into this relationship is still lacking in the context of interdisciplinary subjects. This study investigated the relationship between the classroom learning environment and student achievement in an interdisciplinary subject (i.e. liberal studies) in Hong Kong secondary schools. The mediating role of critical thinking was also explored. The participants were 410 Hong Kong secondary school graduates. The structural equation modelling analyses indicated that (1) the Content aspect of the classroom learning environment had an effect on the achievement in liberal studies, and this effect was not mediated by critical thinking; (2) the Pedagogy aspect predicted critical thinking skills, which in turn predicted the achievement in liberal studies; (3) the Relation aspect had no significant effects on critical thinking skills and student achievement in liberal studies. Suggestions on enhancing students' high-order thinking skills and achievement in interdisciplinary subjects were provided.