A method was developed for the speciation analysis of metal elements in the oral liquid containing Polygonatum and enzymes. The suspended or soluble metals in the oral liquid were isolated by using a 0.45-μm microporous membrane. The inorganic and organic metal species were purified with a D101 macroporous adsorption resin, and the protein-bound and polysaccharide-bound metals were separated from the organic metal species by acetone and absolute ethyl alcohol extractions, respectively. Microwave digestion-high resolution continuum source flame atomic absorption spectrometry (HR-CS FAAS) was used to determine calcium, iron and zinc in different species. The results showed that there were high contents of calcium (318.80 ± 5.38 μg/mL), iron (17.93 ± 0.28 μg/mL), and zinc (3.50 ± 0.06 μg/mL) in the oral liquid containing Polygonatum and enzymes, and most of these metal elements were soluble. Organic metal species were dominant among the soluble metal elements, with organic calcium, iron, and zinc elements accounting for 54.11%, 49.74%, and 55.40%, respectively, of the corresponding total metal elements in the oral liquid. Protein-bound calcium, iron, and zinc accounted for 16.24 ± 0.39%, 12.42 ± 0.22%, and 13.21 ± 0.29%, respectively, of the corresponding total metal elements in the oral liquid. Polysaccharide-bound calcium, iron, and zinc accounted for 25.07 ± 0.50%, 18.47 ± 0.28%, and 4.35 ± 0.29%, respectively, of the corresponding total metal elements in the oral liquid, showing that the polysaccharide-bound zinc content was lower than that of the other metal species. The proposed method shows a high practical value, providing a scientific basis for the speciation analysis of metal elements and illustrating fundamental data for further study on the functions of the oral liquid containing Polygonatum and enzymes.