The invention provides a yttrium ceramic whisker surface modified zirconium boride-niobium-molybdenum based composite material and a preparation method thereof. The yttrium ceramic whisker surface modified zirconium boride-niobium-molybdenum based composite material comprises a zirconium boride-niobium-molybdenum based composite material body and a surface coating. The specific preparation methodcomprises the following steps that zirconium boride powder, niobium powder and molybdenum powder are dried and mixed and then are placed in a prefabricated die and pressed into a body billet, the bodybillet is placed in a carbon fiber crucible after being dried and then is sintered in dynamic vacuum, when the temperature rises to 1700-1900 DEG C, pressurizing is conducted on the body billet, heatis preserved, temperature rising and pressurizing continue, heat is preserved, then the body billet is naturally cooled to the room temperature, and the zirconium boride-niobium-molybdenum based composite material body is obtained; and the zirconium boride-niobium-molybdenum based composite material body is totally impregnated in a surface modifying solution containing yttrium ceramic whiskers and then is taken out for still standing, impregnation is repeated for 2-3 times, drying and calcination are conducted, and the yttrium ceramic whisker surface modified zirconium boride-niobium-molybdenum based composite material is obtained. According to the prepared yttrium ceramic whisker surface modified zirconium boride-niobium-molybdenum based composite material, the strength is high under theultra-high temperature, and corrosion resistance and oxidation resistance are good.