This study explored the interrelationships between students’ general science achievement, scientific epistemoiogical beliefs and their cognitive structure outcomes derived from instruction of basic atomic theory. Research data were mainly gathered from 48 Taiwanese eighth graders’ questionnaire responses and their recalled scientific information about the atomic model, analysed by a flow map technique as evidence of their cognitive structures. This study revealed that students’ science achievement was correlated with many of the students’ cognitive structure outcomes; however, their scientific epistemoiogical beliefs were also significantly related to the structure of knowledge recall, following their listening to a replay of their prior elicited recall. Students holding more constructivist‐oriented views about science tended to recall more information, as well as show more richness, more flexibility and a higher precision of knowledge recall, indicating they had a better metacognitive ability when reconstructing their ideas than respondents having empiricist‐aligned epistemoiogical beliefs. However, those students having constructivist‐oriented epistemoiogical orientations tended to have a slower information retrieval rate.