As a great invention in the Neolithic age, painted pottery culture changed the aesthetic way of ancient ancestors. And the famous Yangshao culture with its painted pottery’s beautiful shape, bright colors and rich ornamentation reveals the artistic features of the original and carries important social and cultural information in prehistoric times. With the accurate, nondestructive and micro damage characteristics of modern spectral analysis technology, it can provide more scientific support for the research on preservation of cultural relics. This paper makes a comprehensive analysis of the painted pottery bowls of Yangshao culture unearthed from Miao-di-gou site dated to the late Neolithic period in Shanxian county, Sanmenxia, Henan province with optical three-dimensional scanning, self-built multispectral imaging, X-ray fluorescence spectrometer (XRF) and laser Raman spectroscopy. The physical and chemical information of the painted pottery is obtained. The digital model of painted pottery bowls are constructed by three-dimensional scanning technique, and the geometric dimension of the samples is non-contacted measured and virtual restoration of digital images of samples are obtained. The similar regions of the chemical characteristics of the sample surface are distinguished from the gray image obtained by multispectral imaging. The chemical compositions and pigment phases of the painted pottery are determined by X-ray fluorescence spectrometer (XRF) and laser Raman spectroscopy. Based on the results of comprehensive research, a digital model of multi-source information of painted pottery relics is put forward, which provides basic scientific information for digital protection and display of such kind of cultural relics.