Three-dimensional video microscopy, Raman spectrometer and scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) were employed to analyze the pigments of various colors on a sample of bank bill issued in 1945. The results indicated that organic pigments including C. I. Pigment Red 146 and C. I. Pigment Red 53∶1, and inorganic pigments such as cinnabar, parareaglar, χ-phase of realgar, carbon black and Prussian blue were used in printing; the brown-black handwriting letters were speculated to be formed from the fading black-blue ink. Most areas of the bank bill were in one single color with one pigment, but two areas of orange-red seals were checked to be colored with cinnabar and two different phases of realgar, and the parareaglar, and χ-phase of realgar were found to be used as printing pigments firstly. This study shows that combining with three technologies above-mentioned is viable and it has great application potential in non-destructive identification of organic and inorganic pigments on paper-based cultural heritage.