The invention relates to super molecule composition of water solubility coenzyme Q10 and the preparation method thereof, the super molecule composition has better curative roles to cardiovascular disease, hepatitis, immunity down and other diseases. The invention belongs to medicine and health care product technical fields. The super molecule composition comprises the following raw materials by the weight parts: coenzyme Q10: cyclodextrin:emulsifying agent is equal to 1:1-50:0.1-10. In aqueous medium, the Q10 super molecule composition is prepared through being mixed by a high speed homogenizer or supersonic oscillation or the homogen of colloid mill, and through the homogen of a high pressure homogenizer, and through being sprayed and dried or cooled and dried, and granulated at last. The composition has higher solubility and digestion degree, the stability is good, the availability relative to the organism is higher.