This study examined 48 Taiwanese 14 year olds' cognitive structures derived from the instruction of basic atomic physics. Content analyses of these students' information processing operations displayed in cognitive structures revealed that even academically above‐average students, in general, used relatively lower‐level modes of knowledge construction, focusing on reciting or describing specific factual knowledge in physics. Students spent more retrieval time when phrasing an idea in a higher‐order cognitive operation, such as in the mode of generalization or conditional inference. Moreover, higher achievers tended to have a richer store of knowledge frameworks, as well as to employ a more inclusive way and a variety of cognitive reasoning manners in structuring their ideas. Students holding scientific epistemological beliefs more orientated to constructivist views of science tended to use more conditional inferential reasoning than those having empiricist‐aligned views of science.