Many research studies have shown that lower-secondary school students' scientific literacy depends on their understanding of corresponding scientific concepts. Therefore, it is of great significance to model and assess students' conceptual understanding in learning specific scientific concepts, because it can reflect and diagnose students' cognitive characteristics, so as to provide evidence for targeted educational interventions. However, on the topic of Moon Phases, existing research studies have deficiencies in the evaluation and analysis of different levels of students' conceptual understanding, which restrict teachers to take effective educational interventions to help them. Thus, this study explored a new level division and an assessment test for revealing and explaining students' different conceptual understanding in learning Moon Phases. This study was conducted among 768 Chinese lower-secondary school students. Through a variety of quantitative and qualitative analyses, it was found that students' conceptual understanding of Moon Phases can be divided into three levels of continuous improvement, including the mechanical memory of different phenomena of moon phases, the formation of a preliminary mental model of Moon Phases, and the construction of a complete mental model of Moon Phases. Accordingly, this study made some precise suggestions for effectively improving students' conceptual understanding of Moon Phases.