The unearthing of a large number of red-yellow colored stones in Yuhui Site, Bengbu city, Anhui province of China, which was the only site of Longshan culture appointed by “Origin of the Chinese Civilization Project” in the Huaihe River basin, has drawn a widespread attention in archaeology. The present research was undertaken to examine elements, mineral composition and thermal history of one red-yellow color stone in different positions, classified according to specialized colors, by means of synchrotron radiation X-ray fluorescence (SR-XRF), X-ray diffraction (XRD), laser Raman spectroscopy (LRS), electron probe micro-analysis ( EPMA ) and thermoluminescence (TL). The results show that the main body of the color stone is limonite with a large amount of quartz inclusion. The yellow substances on the surface layer of the color stone were identified as goethite (α-FeOOH), and the red ones as red ochre (α-Fe2O3+clay+silica). The internal yellow brown substances inside the stone are mainly aphanitic goethite with a number of chromites and manganese dioxide, and also with small quantity of barite and bismuth. And the color stones are without historical firing treatment. These kinds of special polymetallic ores with unique nature and complex geologic history, which were unearthed in the late neolithic site with large numbers, may be closely related to some kind of primitive religious beliefs and special sacrificial practices.