Xanthine can be converted into uric acid, and a high concentration of xanthine in the human body can cause many diseases. Therefore, it is important to develop a sensitive, simple, and reliable approach for measuring xanthine in biological liquids. Hence, a ratiometric surface-enhanced Raman spectroscopy (SERS) sensing strategy with one signal probe was exploited for reliable, sensitive, and quantitative monitoring of serum xanthine. 3-Mercaptophenylboronic acid (3-MPBA) was used as a typical reference with a Raman peak at 996 cm-1. First, 3-MPBA was bound to gold nanoflowers@silica (GNFs@Si) through Au-S bonds. Xanthine oxidase (XOD) catalyzed the oxidation of xanthine into H2O2 on GNFs@Si. Afterward, the obtained H2O2 further reduced 3-MPBA to 3-hydroxythiophenol (3-HTP) accompanied by the emergence of a new Raman peak at 883 cm-1. Meanwhile, the Raman intensity at 996 cm-1 remained constant. Therefore, the ratio of I883/I996 increased with the increasing of xanthine concentration, thus realizing quantitative detection of xanthine. As a result, a ratiometric SERS sensor for the detection of xanthine was proposed with a detection limit of 5.7 nM for xanthine. The novel ratiometric SERS sensor provides a new direction for analyzing other biomolecules with high sensitivity and reliability.