The invention discloses a preparation method of a mullite whisker in-situ toughened chromium phosphate aluminum wave-transmitting material. The method is characterized by the following steps of: dissolving a phosphorus-containing compound into absolute ethyl alcohol or water, adding an aluminum-containing compound and a chromium-containing compound at the temperature of 50-100 DEG C while stirring for reacting, and adding ammonia water, citric acid or methanol for reacting to obtain a chromium phosphate aluminum precursor; putting the chromium phosphate aluminum precursor, the aluminum-containing compound, a silicon-containing compound, aluminum fluoride and water or alcohol into a ball milling device for performing ball milling to obtain a mixture; and drying the mixture, grinding, sieving, performing press forming on the minus sieve, i.e., sintering precursor powder, and calcining in an enclosed container at the temperature of 1,200-1,500 DEG C for 1-24 hours to obtain the mullite whisker in-situ toughened chromium phosphate aluminum wave-transmitting material. The method has the advantages of in-situ growth of mullite whiskers, uniform distribution of the whiskers, dense substrate sintering, good toughening effect, high performance of the wave-transmitting material, applicability of the wave-transmitting material to antenna covers of flying vehicles, radar antenna covers and the like.