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Direct detection and characterisation of small materials are fundamental challenges in analytical chemistry. A particle composed of dozens of metallic atoms, a so-called subnano-particle (SNP), and a single-atom catalyst (SAC) are ultimate analysis targets in terms of size, and the topic is now attracting increasing attention as innovative frontier materials in catalysis science. However, characterisation techniques for the SNP and SAC adsorbed on substrates requires sophisticated and large-scale analytical facilities. Here we demonstrate the development of an ultrasensitive, laboratory-scale, vibrational spectroscopic technique to characterise SNPs and SACs. The fine design of nano-spatial local enhancement fields generated by the introduction of anisotropic stellate-shaped signal amplifiers expands the accessibility of small targets on substrates into evanescent electromagnetic fields, achieving not only the detection of isolated small targets but also revealing the effects of intermolecular/interatomic interactions within the subnano configuration under actual experimental conditions. Such a development of “in situ subnano spectroscopy” will facilitate a comprehensive understanding of subnano and SAC science.