In the face of a highly competitive tourism market, when tourists hold positive brand equity towards a destination, it enhances the destination’s ability to differentiate itself from competitors. This study focuses on the brand equity of organic agricultural tourism, using multidimensional scaling (MDS) to explore the factor structure of brand equity and the perceptual positioning of various tourism destination brands. The research targets tourists engaging in organic agricultural tourism in the Hualien and Taitung regions, with 220 valid questionnaires collected. The research findings indicate the following: 1. Among the 22 brand equity items, “loyalty to organic agricultural tourism”, “awareness of organic agricultural products”, “quality of organic agricultural products”, “environmental sustainability”, “image of healthy tourism”, and “recognition of organic agricultural development” scored the highest. 2. The analysis revealed that the brand equity factors are ranked in the following order: BIHS, BACI, BPQ, BLO, and BAW. 3. Through MDS analysis, the five organic agricultural tourism destinations were categorized into high, medium, and low brand equity groups, illustrating the differentiated competitive relationships among these destinations. The top three factors influencing the brand perceptual maps were BAW, BIHS, and BPQ. The results of this study can serve as a reference for future research on brand equity in organic agricultural tourism and provide a scientific basis for the practical application of shaping brand equity and formulating competitive strategies.