The invention belongs to the technical field of an advanced composite material science, and particularly relates to a boride ceramic in-situ filling cyanate ester resin base composite material and a preparation method thereof. By an in-situ polymerization method, firstly, bisphenol A is dissolved in a benzene or alkane type organic solvent; a certain amount of cyanogen halide is added; mechanical stirring is performed in an environment being -10 to 0 DEG C to obtain a mixed solution; under the strong stirring, metal boride ceramic powder is added into the mixed solution; the stirring is continuously performed; at -10 to 0 DEG C, triethylamine is dropwise added into the system; the system takes polymerization; after the organic solvent is removed through distillation, metal boride powder in-situ filling cyanate ester resin is obtaine; then, a catalyst is added for stirring; after vacuum degassing treatment, curing formation is performed at a high temperature. The prepared metal boride in-situ filling cyanate ester resin base composite material has the structure performance characteristics of uniform material tissue, heat resistance and excellent heat conduction performance, and can be used as a base board material, an encapsulating material and the like of a printed circuit board in electronic equipment for space navigation industry and aerospace industry.