The invention discloses a preparation method of a pervaporation composite membrane filled with hydrophobically modified nano calcium carbonate. The preparation method of the pervaporation composite membrane filled with hydrophobically modified nano calcium carbonate comprises the following steps: (1) adding dried nano calcium carbonate into oleic acid, stirring for reacting, then repeatedly washing with hexane for removing excess oleic acid,, drying in vacuum, and grinding so as to obtain hydrophobically modified nano calcium carbonate; (2) mixing dried polyvinylidene fluoride with hydrophobically modified nano calcium carbonate, subsequently adding the mixture into dimethylacetamide, carrying out ultrasonic dispersion, stirring, filtering, standing and defoaming, and subsequently pouring the obtained liquid on a polyester non-woven fabric for scraping a membrane so as to obtain a modified polyvinylidene fluoride base membrane by using an immersion precipitation phase inversion method; and (3) dissolving polydimethylsiloxane in n-hexane, adding hydrophobically modified nano calcium carbonate, carrying out ultrasonic dispersion, adding a cross-linking agent and a catalyst, stirring for reacting, centrifuging and dedoaming, subsequently pouring the obtained liquid on the polyvinylidene fluoride base membrane for scraping the membrane, airing and drying the membrane in vacuum to prepare the pervaporation composite membrane. The composite membrane prepared by the method is simple in process and low in cost, and moreover, the selectivity and the flux of the composite membrane on alcohol are improved.