Palygorskite (PAL) was treated with HCl to prepare pickling palygorskite (PA), and modified PAL (PCS, PDO, PKH) were prepared by organic modification of PA (chitosan, cationic surfactant dioctadecyl dimethyl ammonium chloride, silane coupling agent KH550). Finally, modified palygorskite/sappanwood hybrid pigments (short for hybrid pigment, the same as full text) PAS, PCSS, PDOS, PKHS were prepared by PA, PCS, PDO, PKH loaded with sappanwoood dye extract. Through FTIR, XRD, TEM, BET, TG and color characterization, the effects of different modification methods on the powder properties, stability and biosafety of the prepared hybrid pigments were investigated. The results showed that organic modification and sappanwoood dye extract loading do not change the crystal structure and fiber morphology of PAL. The hybrid pigments significantly improved the thermal stability, acid-base stability and covering power of sappanwoood dye extract. Hybrid pigment (PCSS) prepared by chitosan modified PAL showed better comprehensive properties: thermal stability (ΔE<6 on exposure to 120 ℃ for 6 h), the best acid-base stability (ΔE<4 on soaking in pH=5~9 solution for 24 h), the lowest water-alcohol dissolution rate (2.13 mg/g in water and 1.02 mg/g in ethanol), high biosafety (non-irritant to vascular membrane).