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In archeology, pottery represents an important class of artifacts giving information on the past human activity, the ecology, and ancient cultural groups. Some chemical analytic methods, including X‐ray fluorescent analysis, were adopted for the archeological study of pottery. However, these techniques also involve problems, including the destructive analysis of materials, and cannot analyze the original clay condition of pottery. To address this, we carried out nondestructive chemical analysis of 13 potsherds excavated from the Yaeyama Islands in the southern Japan archipelagos using X‐ray fluorescence microscopy. Two analytic methods were used, elemental mapping and multipoint spectral measurement, making it possible to obtain a visualized elemental distribution on potsherd surface and a detailed multipoint elemental composition of the same sample for the multivariate statistical analysis. In this study, the visualized images suggested that calcium particles were mixed to temper the materials, and their size and quantity differed between potsherds, whereas the uniformity of clay substrate, including the quantities of iron and silicon on multipoint measurement, was a characteristic of each potsherd. Therefore, principal component analysis and nonmetric multidimensional scaling analysis of the potsherds suggest that the differences between the Yaeyama Islands in terms of pottery manufacturing technology are due to chronological factors in this case. Our method represents an effective new approach to the pottery study for technological change.