Pigments play a pivotal role in the cosmetic industry, in which the development of pigments with concurrent color diversity, hydrophobicity, biocompatibility and photostability remains a great challenge. Herein, we report organic-inorganic composite pigments synthesized via a combination of organic dye anions (Ponceau SX and acid green (AG)), layered double hydroxides (LDHs) and octyltriethoxysilane (OTEOS) (denoted as O/Dye-LDHs: O/SX-LDHs and O/AG-LDHs).The prepared composite pigments were characterized via a comprehensive investigation based on X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS-mapping), Fourier transform infrared (FT-IR) spectroscopy, CIE 1976 L*a*b* color scales, static contact angle measurement and HET-CAM assay. The results confirm the successful intercalation of organic dye anions into the interlayer region of LDHs via host-guest interactions and the surface modification of OTEOS on the layer surface, forming a new kind of hydrophobic organic-inorganic composite pigment with a sandwich structure. LDH layer protection and OTEOS coating play crucial roles in the high photostability, good hydrophobicity and satisfactory biocompatibility of pigments. In addition, O/Dye-LDHs exhibit rich color and color adjustability. Impressively, we applied mixture composite pigments with different O/SX-LDH-to-O/AG-LDH ratios to formulate an eye shadow cream, which present a series of popular and natural colours with water resistance to enhance one's attractiveness and appearance. This work provides a promising strategy for the design of safe and efficient composite pigments, demonstrating their potential application in the field of makeup.