Spatial thinking is ubiquitous in design. Design education across all age groups encompasses a range of spatially challenging activities, such as forming and modifying mental representations of ideas, and visualizing the scenarios of design prototypes being used. While extensive research has examined the cognitive processes of spatial thinking and their relationships to science, technology, engineering, and mathematics learning, there remains a knowledge gap regarding the specific spatial thinking processes needed for open-ended problems, which may differ from those assessed in close-ended, analytical spatial tasks. To address this gap, we used educational design-based research to develop a nature-inspired, design-by-analogy project and investigate the spatial thinking processes of young, novice designers. 16 children from an international school in the Netherlands participated in this five-week design project. Multimodal evidence from classroom recordings and children’s design works were triangulated to offer insight into the key spatial thinking processes involved in their creation of nature-inspired, analogy-based design prototypes. Our results revealed spatial thinking processes that might not align with those assessed in conventional spatial tests and may be unique to design or open-ended problem-solving. These processes include abstracting spatial features to infer form-function relationships, retrieving a range of relevant visual information from memory, developing multiple possible analogical matches based on spatial features and relationships, elaborating and iterating on the design concepts and representations to make creative and suitable solutions for the design challenge, as well as visualizing design prototypes in practical usage scenarios. By highlighting the nuanced differences between spatial thinking in open-ended, divergent thinking tasks and conventional spatial tasks that demand single correct solutions, our research contributes to a deeper understanding of how children utilize spatial thinking in design and open-ended problem-solving contexts. Furthermore, this case study offers practical implications for scaffolding children's analogical reasoning and nurturing their spatial thinking in design education.