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The purpose of this research is the design and implementation of a support system for learning programming. To archive this purpose, in this article, we propose a Puzzle Programming System that uses jigsaw puzzles as an example of the application of physical visualization, which visualizes logical constraints to physical ones. This Puzzle Programming System aims to teach basic programming concepts by presenting the invisible constraints of programming language syntax using the visual constraints of jigsaw puzzle pieces. This system runs on an Apple iPad and was developed using the Unity game engine. We used YAML as a data format for serializing structured data for data management. By inviting high school students to try out a prototype, we could confirm the usefulness of the Puzzle Programming System. The experimental evaluation results also shed light on aspects of the game that need to be redesigned and parts where the visual programming model needs to be modified and expanded.