The relationship between trace elements in coal and organic functional groups of coal, also some of aromatic structure, was investigated by using curve fitting of infrared spectra. Cluster analysis was also performed according to the degree of affinity of organic groups to the trace elements. The results show that there is a possibility that trace elements, especially LREE, were bound to peripheral organic functional groups of middle rank coal macromolecule. The most possible functional group that binds trace element is the hydroxyl, and to the less degree, the asymmetric -CH3 and >CH2 stretching, -CH3 stretching, etc. The degree of affinity of trace elements to different functional groups varies. The tendency obeys the natural structural changing law of trace elements—the periodic law. The deviation of some trace elements from this regular trend is attributed to the deviation of intrinsic “confusion degree” (conventional molar entropy) of the matter system of coal basin, which is affected by the inner and outer factors during the evolution.