The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling technique. The same number of students formed the control group. In the experimental class, the learning was conducted by using multiple representations, whereas the control classes undertook conventional learning. Result of the research shows that (1) Learning with multiple representations is more effective in constructing students' mental models in understanding the concept of atomic structure compared with the conventional learning; (2) Learning with multiple representations is suitable for lessons in classes where the students have low capability level to keep up with those who have a medium and high capability level. These findings indicate that lessons, which involve the macro-sub-micro-symbolic phenomena using multiple representations, may improve their mental model and effectiveness of atomic structure studies. The learning model is discussed as an alternative in class lessons in order for the students with initially low capability to keep up with those of medium and high capability in constructing their mental models.