Against the backdrop of the transformation of educational approaches in the new era and the deepening of the new curriculum reform, interdisciplinary thematic learning has become an important approach to cultivating students’ core competencies and enhancing their ability to adapt the complex real-world challenges. Focusing on the goal of developing integrated thinking, this paper takes karst landforms as the teaching context to construct a systematic interdisciplinary instructional design integrating geography and chemistry. By transforming invisible microscopic chemical processes into perceptible learning experiences, it helps students establish a cognitive chain of landform formation. A four-stage interdisciplinary framework of“phenomenon description–microscopic mechanism–macroscopic evolution–human– environment relationship”is developed, together with a teaching evaluation rubric aligned with the three dimensions of integrated thinking, providing a practical reference for interdisciplinary teaching in physical geography.