Augmented Reality (AR) has been identified by educational scientists as a technology with significant potential to improve emotional and cognitive learning outcomes. However, very few papers highlighted the technical process of creating AR applications reserved for education. The following paper proposes a method and framework for how to set up an AR application to teach primary school children the basic forms and shapes of atoms, molecules, and DNA. This framework uses the Unity 3D game engine (GE) with Vuforia SDK (Software Development Kit) packages combined with phone devices or tablets to create an interactive App for AR environments, to enhance the student’s vision and understanding of basic chemistry models. We also point out some difficulties in practice. As for those difficulties mentioned, a series of solutions plus further development orientation are put forth.