The invention relates to a preparation method of heat-conductive epoxy resin. The preparation method comprises the following steps: (1) stirring and mixing natural flake graphite with concentrated sulfuric acid, then, adding KMnO4 and NaNO2 and continuing to stir; dropwise adding distilled water to dilute, adding an H2O2 solution, washing to be neutral, carrying out vacuum drying and ball-milling to obtain GO; (2) preparing an ethanol solution, adding a KH550 silane coupling agent, then adding GO to prepare a solution, and after ultrasonic and reflux treatment, washing to be neutral and drying to obtain GO-KH550; and (3) heating EP in an oil bath, then, adding the ethanol solution of GO-KH550, raising the temperature, adding 2-ethyl-4-methyl imidazole, ultrasonically stirring, and then injecting into a die, putting into a vacuum box to exhaust and curing to obtain the heat-conductive epoxy resin. The natural flake graphite provided by the invention is used in an EP packaging material and the heat conductivity and heat stability of the natural heat-conductive epoxy resin are remarkably improved.