Covering with polyorganosilane (POS) was proved as an effective way to enhance the chemical and thermal stability of clay/dye hybrid pigments. But the photostability and interactions with clay minerals, dyes and POS layer has never been reported. In order to investigate above issues, new organic-inorganic hybrid pigments based on halloysite (Hal) and indigo (In) were prepared by grinding method. X-ray diffraction, transmission electron microscopy, thermogravimetry, Fourier transform infrared spectroscopy were applied to characterize the structure of In-Hal (without POS layer) and In-Hal-POS (with POS layer) pigments. Solid state nuclear magnetic resonance (NMR) was employed to reveal the interactions between Hal, In and POS. Reflection spectra and CIE 1976 color space system were used to evaluate the color parameters and color changes of pigments. Thermal stability, chemical resistance to ethanol, 1 mol·L−1 HCl and 1 mol⋅L−1 NaOH, and light fastness to visible light were tested. Indigo molecules dispersed on the surface of Hal nanotubes. POS layer homogeneously covered on the surface of hybrid pigments, without changing the crystal structure and morphology of Hal. Covering with POS layer seldomly affect the color of hybrid pigments. However, In-Hal-POS exhibited better stability than In-Hal, due to hydrophobic surface which can prevent indigo molecules from chemical reactions and degradation. A new route was proposed to prepare organic-inorganic hybrid pigments, ignoring the interaction between dye molecules and substrates.