The pigments have advantages on thermal stability, light resistance and chemical resistance, so they are wildly applied to manufacturing color filters. However, the color filters manufactured with pigments have introduced spectral drawbacks such as decreased transmittance of light and decreased contrast ratio (CR) both caused by organic nano-pigments. Among the three primary colors, green one has the highest brightness and the greatest effect on CR. In this study, our focus is on a green color filter with wide color gamut, which mainly contains three pigments, such as pigment green 58 (G58), pigment yellow 138 (Y138), and pigment yellow 185 (Y185). The Y185 with high tinctorial strength has been introduced to effectively reduce the color filter thickness, but the CR is decreased. In this paper, the effect of scattering and fluorescence on CR of Y138 and Y185 are analyzed. The size, n (refractive index), crystal structure, morphology and fluorescence properties of these two kinds of pigments have been compared. The results show that the aggregation of Y185 organic nano-pigments in CF manufacturing process is the main reason, which leads to the lowered CR. By systematically investigating the effects of the organic nano-pigments on CR, this paper provides a theoretical basis and guidance for realizing the CFs with high CRs by designing organic nano-pigments.