Size/scale is a central idea in the science curriculum, providing explanations for various phenomena. However, few studies have been conducted to explore student understanding of this concept and to suggest instructional approaches in scientific contexts. In contrast, there have been more studies in mathematics, regarding the use of number lines to relate the nature of numbers to operation and representation of magnitude. In order to better understand variations in student conceptions of size/scale in scientific contexts and explain learning difficulties including alternative conceptions, this study suggests an approach that links mathematics with the analysis of student conceptions of size/scale, i.e. the analysis of mathematical structure and reasoning for a number line. In addition, data ranging from high school to college students facilitate the interpretation of conceptual complexity in terms of mathematical development of a number line. In this sense, findings from this study better explain the following by mathematical reasoning: (1) varied student conceptions, (2) key aspects of each conception, and (3) potential cognitive dimensions interpreting the size/scale concepts. Results of this study help us to understand the troublesomeness of learning size/scale and provide a direction for developing curriculum and instruction for better understanding.