Multidimensional scaling can be used to identify relationships among concepts, revealing the structure of the cognitive framework by measuring distances within perceptual maps. The current study sought to examine the relationships among concepts related to photosynthesis in 2,844 $3^{rd}-11^{th}$ grade science students. The questionnaire included items on 'location,' 'products,' 'reactants,' and 'environmental factors', presenting images related to each theme. Students provided responses corresponding to particular topics, and reported the extent to which the concept was related to the topic on a scale from 1 to 30. The survey results were as follows: first, students were not able to clearly distinguish between or understand the four main topics. Second, students organized their cognitive structures by closely associating related concepts after learning. Third, the presented concepts revealed a mixture of scientific and non-scientific concepts, suggesting that students needed to clearly distinguish the preconceptions through which they organized concepts, so that they are suitable for cognitive structures based on learning. Furthermore, non-scientific concepts within perceptions were consistently maintained throughout learning, affecting the proximity of scientific concepts.