Learning science offers a theoretical lens for understanding deep learning by focusing on internal cognitive mechanisms. Problem-based Learning drives students to engage in higher-order cognitive activities through real-world situations and problem-solving, serving as a crucial pathway to deep learning. From the perspective of learning science, this paper analyzes the cognitive progression mechanisms and information-processing procedures in high school geography problem-solving, and constructs a cognitive progression model of “surface learning-deep learning-transfer learning.” Taking “the impact of regional development on transport layout” as a case, it designs a PBL instructional plan aligned with the cognitive pathways of problem-solving. The study aims to remedy the prevalent issue of surface-level knowledge acquisition, guide students toward stepwise cognitive progression, foster the occurrence of deep learning in geography, and provide practical references for the cultivation of core competencies in geography.