In 2013, several tombs were discovered and excavated in Southeastern Beijing, China, yielding various burial products. Among these were pottery towers, a representative artifact of the Han Dynasty rarely found in the area. Many studies on architectural aspects, such as construction type and construction situation, have been conducted based on the excavated pottery towers, but only a few have examined their raw materials or pigments. In this study, black, white, and red pigments were identified as carbon black, calcite, and cinnabar, respectively, through a multi-analysis approach. The manufacturing method of the pigment was established based on the crystal form and particle size of the pigment, by factoring in the pigment characteristics, which cannot be distinguished by component analysis and crystal structure analysis. We recommend that a continuous database be prepared and used in the future, not only for an interpretation of ancient pigments but also to identify the factors to be considered (physical characteristics, such as pigment particle size among others) when estimating the manufacturing process and conservation treatment.