The invention discloses a preparation method of a nanocrystallized cotton fiber super-hydrophobic composite material. The preparation method comprises the following steps that 1, alkali washing, primary ball milling, acid washing, secondary ball milling, washing, drying and crushing are carried out on cotton linters to obtain a nanocrystallized cotton fiber; 2, the nanocrystallized cotton fiber isfed into a sodium hydroxide solution, epichlorohydrin is added in the stirring state, and the temperature is adjusted to 65 DEG C-75 DEG C, stirring is carried out for 2-3 h, and filtering, washing and drying are performed to obtain an epoxidized nano-cotton fiber; 3, aminated beta-cyclodextrin and starch-based carbon microspheres are mixed, and wet ball milling, drying and crushing are performedto obtain a starch-based carbon microsphere-cyclodextrin compound; and 4, the starch-based carbon microsphere cyclodextrin compound is dispersed in water, the epoxidized nano-cotton fiber is added under the stirring state and stirred for 10-20 h at the temperature of 70 DEG C-80 DEG C, and filtering, washing and drying to obtain the nanocrystallized cotton fiber super-hydrophobic composite material.