The invention provides a method for preparing biodiesel through catalysis of a natural biomass solid acid catalyst. The method comprises the following steps: 1, washing, drying and crushing the natural biomass, weighing and impregnating the crushed biomass, and taking out and drying the biomass; 2, impregnating acidified biomass in a metal salt solution, taking out and drying; 3, placing the biomass loaded with metal salt in a muffle furnace for roasting to obtain a natural biomass solid acid catalyst; and 4, adding the prepared biomass solid acid catalyst, short chain alcohol and oil into a batch reactor for esterification and an ester exchange reaction; after the reaction, conducting reduced pressure distillation to remove excessive short chain alcohol; and standing to delaminate glycerol and biodiesel produced in the reaction, wherein the biodiesel product is on an upper layer. According to the invention, natural renewable biomass is used as a raw material for direct acidification, without carbonization, so as to realize low cost and high biological diesel oil yield; besides, the prepared catalyst has advantages of good mechanical strength, particle size conducive to recovery, and no secondary pollution.