A family cemetery of the Yuan Dynasty was discovered in Yanta District of Xi’an, and represents one of the important new archaeological discoveries in Shaanxi Province. Residual murals of Tombs M38 and M40 were damaged but brightly colored, still basically retaining the structural information of the pigment layer. In order to understand the mural pigment types of the two Yuan tombs, cross-sectional analysis, microscopic infrared spectrometry, micro-Raman spectrometry, and scanning electron microscopy-energy dispersive spectrometry (SEM-EDS) were used for scientific analysis. The results show that the pigments include mineral pigments and organic dyes:red pigments include red lead, cinnabar and iron red; the black one carbon black; the white one calcite; the green one malachite; blue ones azurite and indigo. The mural of Tomb M38 has a ground layer, but that of Tomb M40 does not. The application of indigo found this time is another use case following the murals of Han Xiu’s tomb of the Tang Dynasty in Xi’an, providing new information for the use of indigo as a painting material for Yuan Dynasty murals. The research results could also provide an important reference for the subsequent conservation and restoration of the murals in the two Yuan Dynasty tombs.