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Subnanoclusters were characterized by elaborated spectroscopic methods revealing distinctive natures of subnanomaterials., Subnanometric metal clusters exhibit anomalous catalytic activity, suggesting innovative applications as next-generation materials, although identifying and characterizing these subnanomaterials in atomic detail remains a substantial challenge because of the severely weak signal intensity for the conventional analytical methods. Here, we report a subnanosensitive vibrational technique established based on the surface-enhanced Raman spectroscopy, demonstrating the first-ever detailed vibrational characterization of subnanomaterials. Furthermore, combining with density functional theory calculations, we reveal that inherent surface structures of the tin oxide subnanoclusters determine the size-specific spectral and catalytic characteristics of these clusters. The high-sensitivity characterization methodology elaborated here can provide a comprehensive understanding of the chemical and structural natures of subnanomaterials, which facilitate the rational design of subnanomaterials on the atomic scale for practical applications, such as in catalysts, biosensors, and electronics.