Recognizing the significant spatial visualization challenges that high school students face in understanding abstract chemical compound structures—a limitation often inherent in conventional teaching methods based on 2D diagrams—this research presents the comprehensive development and user experience (UX) evaluation of an innovative adaptive learning application in Virtual Reality (VR). The application, developed using the Unity 3D engine and configured via XR Plugin Management to ensure broad hardware compatibility, places students in an interactive virtual laboratory. Within it, students can directly manipulate meticulously designed 3D atomic models to build molecules, observe the formation of covalent and ionic bonds, and interact with dynamic chemical processes. Its key innovation is the integration of an intelligent adaptive learning algorithm, which utilizes a Firebase cloud database to analyze user performance metrics—such as accuracy, completion time, and recurring areas of difficulty. Based on this data, the system dynamically personalizes learning pathways by recommending remedial content or more challenging topics. Furthermore, assessment materials such as quizzes were efficiently generated using large language models (LLMs) to ensure relevance and quality. An in-depth UX evaluation was conducted with high school students using a mixed-methods approach, combining standardized questionnaires to quantitatively measure metrics like usability, engagement, and satisfaction, with qualitative feedback sessions for contextual insights. The results indicate a highly positive user experience; participants reported that the ability to directly manipulate molecules in 3D space significantly enhanced their conceptual understanding, bridging the gap between theory and visualization. The adaptive system was highly valued for its ability to adjust to individual learning paces, which was shown to boost confidence and reduce frustration. This research provides strong evidence that VR-based adaptive learning platforms are powerful pedagogical tools, capable of transforming chemistry education by making complex scientific concepts more accessible, engaging, and comprehensible.