The purpose of this study is to analyze the niche overlap and proximity of photosynthetic domain concepts according to the cognitive level of middle school students. For this, the subjects were 204 7th grade students. The cognitive level of middle school students was classified using the questionnaire used in GALT. After that, data on the concept relevance score and understanding level were collected using the concept relevance and understanding level questionnaire. The understanding level analysis framework and analyzed using the classification criteria modified and supplemented by Lim et al. The niche overlap of concepts was visualized using McPherson’s square method using the concept relevance score and understanding level score, and the proximity between concepts was visualized using the multidimensional scaling method. The results of this study are as follows. First, students in the formal operational stage recognized science concepts closely as a result of learning, and the niche overlap between science concepts was high. Second, even after learning, niche overlap and proximity between concepts unrelated to the domain were presented, which differed according to cognitive levels. Third, the same concept had different niche overlap and proximity according to the domains, and there was a difference according to the cognitive level. Through the results of this study, it is necessary to connect and explain related scientific concepts for students with low cognitive levels. In addition, when the same concept is presented in different domains, it is expected that the properties and characteristics of each domain are clearly distinguished and taught.