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Short auditory cues in enclosed built environments (such as elevator calls, access control, navigation, and heating, ventilation, and air conditioning (HVAC) notifications) influence not only usability but also stress and perceptions of well-being in daily indoor life. However, acoustic research remains largely focused on physical properties, and the psychophysiological impact of such short auditory cues remains under-quantified. To address this gap, a neuroscience-based evaluation approach, the Acoustic User Experience and Emotion (AUEX) model, is proposed. This model integrates functional near-infrared spectroscopy (fNIRS), electrodermal activity (EDA), and the User Experience Questionnaire (UEQ). With 33 in-cabin prompt sounds as a controlled typology of short auditory cues in an enclosed setting, we set up a simulated interaction experiment with 20 participants in a driving simulator vehicle cabin to investigate the relationship between acoustic properties and cognitive load, arousal, and user experience. The results show that timbre is the key factor, which was correlated positively with overall UX (r = 0.414) and negatively with prefrontal ΔHbO (CH3: r = −0.368; l-DLPFC: r = −0.449), indicating a decrease in cognitive load and a relaxed affective state. Conversely, high-frequency signals improved pragmatic quality but increased physiological arousal, which negatively affected hedonic assessment. To facilitate the translation of evaluation results into practice, we also completed a design phase that converted the AUEX results into scenario-based parameter targets and prototype designs for functional, warning, and brand/affective cues, illustrating how evidence-based relationships can be translated into design-ready outputs for enclosed built environments. These results confirm the AUEX approach as a transferable method for designing short auditory cues for well-being and provide parameter-level implications for therapeutic and human-centered sound design in smart buildings, intelligent vehicles, and other enclosed built environments. Overall, the AUEX approach provides a transferable evaluation-to-design workflow for short auditory cues in enclosed interactive contexts; however, direct generalization from a single controlled vehicle cabin setting to real-world building environments should be validated through future field studies. Accordingly, the present findings are positioned as evidence from a controlled enclosed case rather than universal conclusions for all enclosed spaces.