The invention relates to the technical field of oral and maxillofacial medical imaging technologies, in particular to a composite cone beam CT enhanced contrast agent which comprises an X-ray imaging agent sodium iodide, distilled water, a hydrophilic medicinal penetrant dimethyl sulfoxide, an organic solvent, a fungicide ethanol, a lipophilic penetrant and a flavoring agent ethyl acetate. The imaging component content of the contrast agent can be adjusted, and the contrast agent can be recognized with different densities of tooth tissues and various fillers, so that the accuracy, sensitivity and specificity of CBCT on tooth subfissure diagnosis are further improved; a preparation method of a composite cone beam CT enhanced contrast agent comprises the following steps: firstly, slowly dissolving 25 g of 99% dimethyl sulfoxide in 10 g of distilled water, stirring and dissolving to obtain a homogeneous solution, then adding 10 g of 99% ethanol, stirring and dissolving to obtain a homogeneous solution, then adding 10 g of 99% ethyl acetate, stirring to obtain a homogeneous solution, and finally adding 10 g of 99% ethyl acetate, stirring to obtain a homogeneous solution; finally, 30 g of 99% sodium iodide is added and dissolved into a homogeneous solution, and compared with meglumine diatrizoate, the contrast agent prepared through the method has the advantages that the developing rate and the developing depth are obviously improved.