The purpose of this study is to design and implement a digital simulation-based lesson supporting structural knowledge formation in elementary social studies on transportation and to explore learners’ thinking patterns and teacher reflections. To address this, a digital simulation lesson utilizing an agent-based model (ABM), grounded in relational thinking and a systems approach, was applied to a third-grade class. This self-study had the teacher reflectively explore a personally designed lesson. Data included student utterances, worksheets, causal cycle maps, observation records, and teacher logs, repeatedly reviewed to interpret learners' relational representations. Findings showed learners' thinking reorganized around temporality, extensibility, and cyclicality — expanding from immediate to delayed processes, from isolated elements to broader social and environmental networks, and from one-way causality to feedback-loop structures. Learners explained structural relationships using arrows, explanatory sentences, and policy-change comparisons, while the teacher’s role shifted from knowledge transmitter to cognitive designer. This study suggests digital simulations can function as mind tools supporting relational thinking and structural knowledge formation in elementary social studies, with implications for teaching complex social phenomena.