The invention discloses a method for preparing a saliva protein sample, and belongs to the technical field of preparation of saliva protein samples. The method is characterized by comprising the following steps of: 1) collecting saliva; 2) centrifuging 800g of collected saliva at 4 DEG C for 15 minutes, and sucking supernate; 3) adding 0.05 to 5 volume percent acetic acid and uniformly mixing; 4)centrifuging 14,000g of the mixed solution at 4 DEG C for 60 minutes, and sucking supernate; 5) putting the supernate in a dialysis bag, and dialyzing by using double distilled water for 5 hours; and6) condensing to obtain the saliva protein sample. The method has the advantages of high protein recovery rate, short preparation time, safety, nontoxicity, increase of loading quantity of low abundance proteins, clear and easily analyzed maps and the like.