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In this study, we presented a design-based research program that aims to design and investigate an integrated learning environment that organically integrated physical experiments and virtual tools. Relying on theory of concreteness fading, we use infrared imaging and learning analytics to argument students’ interaction with the physical materials. Through two iterations of design and testing, we found that students actively used of the virtual tool during their physical experiment process. This integrated learning environment can help students highlight salient information and removing confusing details and further develop students’ conceptual understanding of thermal concepts. Through this iterative development process, we also synthesized design principles and factors to consider when design and implement integrated learning environment to support students’ learning.