The invention discloses a method of determining selenium shape of honey and fruit juice by solid phase extraction-atomic fluorescence spectrometry. The method comprises the following steps: separating organic selenium and inorganic selenium in honey or fruit juice under a condition of pH being 3 by means of an SCX solid phase extraction column; then adding a mixed acid to digest and separate to obtain an inorganic selenium extraction liquid; then determining the selenium element by means of atomic fluorescence spectrometry; determining the content of total selenium by means of wet digestion; and finally obtaining the content of the organic selenium by means of a minusing method. The method of determining the shape of selenium separates and determines inorganic selenium and organic selenium accurately and effectively by combining technologies of ionic adsorption exchange, acid digestion and atomic fluorescence spectrometry and the like. The method is simple, environmentally friendly and efficient, thereby providing a powerful technical support for evaluating the functionality and safety of selenium-enriched honey and juice.