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A major goal of education is to help students retain as much meaningful information as possible for long periods of time. The learning process by which students acquire new knowledge and behaviors is closely related to memory, which is the core of cognition. In a previous study, we developed virtual reality visualization model (VRVM) that can be applied to address difficulties with learning medical biochemistry. Validation and evaluation studies are necessary to assess the usefulness of VRVM. The purpose of the present study is to apply VRVM and evaluate its effectiveness in a real educational environment. We modeled and verified the concept of spatiotemporality of information obtained through VRVM, which augments memories in linkage with hippocampal-centered networks while helping students to transition to higher-order thinking. The effectiveness of VRVM of the tricarboxylic acid (TCA) cycle, an onerous topic for medical students, was compared with that of traditional educational methods. The experimental group used VRVM to learn the TCA cycle, while the control group learned from PowerPoint (Microsoft Co., Redmond, WA, USA) presentations using 2-dimensional (2D) diagrams. Evaluations of short-term and long-term memory indicated that learning using VRVM was more effective than learning through traditional lecture-based methods, and that VRVM resulted in better recall compared to traditional methods. Our findings suggest that VRVM can be applied when teaching students about the complicated TCA cycle, and that it helps medical students to improve their recall of carbohydrate metabolism in the context of medical biochemistry studies.