A systematic literature review across multiple scientific disciplines was conducted to explore students' understanding of atomic structure, focusing on students' ACs. A total of 112 publications between 1972 and 2023 were selected for the study. Within the selected body of literature, 851 instances of ACs were distributed across students ranging from third grade to graduate‐level physical chemistry. As students' atomic structure understanding becomes more sophisticated, multiple intermediate atomic structure models were described in the path from a pre‐atom understanding of the composition of matter to a quantitative understanding of the atom's quantum‐mechanical characteristics. A series of construct maps were created for each intermediate atomic structure model, organizing students' ACs in a sophistication hierarchy, and using threshold concepts as capstones. Each construct map level is described and selected ACs that exemplify each construct map sublevel of understanding are discussed. The series of construct maps encompass a model of student understanding to diagnose students' level of understanding of atomic structure. This work intends to highlight students' different levels of understanding for the structure of the atom, with the assumption that student knowledge can deepen in sophistication from students' current knowledge. This work opens the possibility of designing an instrument to assess students' understanding of atomic structure using an ordered multiple‐choice approach.