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Algebra is mandatory learning in junior high school. That is a continuation of arithmetic with the bridge being variable. Students often have difficulty in understanding it, especially quadratic equations. The purpose of this study is how students cognitive processes in understanding the principles of quadratic equations. It was an exploratory study conducted on research subjects. The subjects were junior high school students selected based on their ability to understand concepts and principles about quadratic equations. Thats done through tests about understanding quadratic equations. There were 16 selected research subjects. They were interviewed in-depth by researchers using interview guides. Interview data were analyzed qualitatively based on genetic decomposition. The results of this study are that students can use square, rectangular and unit square cards to determine the principle of factorization of quadratic equations. Students can generalize until completing a perfect quadratic equation. The conclusion is that the cognitive process of students who learn to use learning media based on square and rectangular able to reach a high level (trans-level).