Abstract: Digital intelligence technology is a comprehensive technical system with data as the key element and artificial intelligence as the core driving force. It provides innovative methodological support for addressing core bottlenecks in rare disease etiology research, including sample scarcity, high-dimensional datacomplexity, intricate pathogenic mechanisms, and challenges in causal validation. This paper systematically reviews the application pathways and current implementation of digital intelligence across four major stages of rare disease research, including etiological clue mining, causal inference, mechanism analysis, and clinical translation. Furthermore, it summarizes the technical strengths, existing limitations, and developmental challenges, aiming to inform optimization of the research paradigm and promote the sustainable advancement of rare disease research.