Geography education requires a combination of knowledge, skills, and geospatial relational thinking. To improve the learning efficiency and durability of knowledge, a new inquiry-based instruction system using tangible user interfaces has been developed. The tangible landscape modeling system (TLMS) comprises four components including a malleable physical model, 3D scanner, projector, and standard computer with software. In this paper, we introduce the TLMS for geography themes from a primary to a tertiary education level. We present a case study conducted for the secondary level of education in a local school with 8 children at the age of 11 years from a marginalized community. The TLMS is applied to typical geography themes with topographic maps, land surface and landscape processes such as water flow and flooding phenomena, often poorly understood by students. These examples are documented by the experiment setups and description of the workflow steps. Results of this study showed an improved understanding of the concept of contours and basic landforms. This indicates that the tangible landscape modeling system provides an easy-to-understand concept and teaching tool that improves the geospatial relational thinking of students.