The invention discloses a zinc oxide whisker/graphene nanosheet synergistically modified cyanate ester resin heat conduction composite and a preparation method thereof. The composite comprises the following raw components in parts by mass: 100 parts of cyanate ester resin, 10-50 parts of inorganic fillers and 2.0-7.5 parts of modifier, wherein the inorganic fillers include zinc oxide whiskers and graphene nanosheets in a mass ratio of (2 to 1)-(1 to 10); the modifier is 2,2'-diallylbisphenol A. The heat conduction composite is obtained through prepolymerization and casting moulding and curing after mixing the inorganic fillers with the resin by a melting method. The obtained modified cyanate ester resin heat conduction composite has excellent heat conduction property and also has excellent heat stability and good electrical insulating property.