Enrichment and quantification of sugar phosphates (SPx) in biological samples were of great significance in biological medicine. In this work, a series of zirconium-based metal−organic frameworks (MOFs) with different degrees of defects, namely, HP-UiO-66-NH 2 -X, were synthesized using acetic acid as a modulator and were utilized as high-capacity adsorbents for the adsorption of SPx in biological samples. The results indicated that the addition of acetic acid altered the morphology of HP-UiO-66-NH 2 -X, with corresponding changes in pore size (3.99−9.28 nm) and specific surface area (894.44−1142.50 m 2 •g −1 ). HP-UiO-66-NH 2 -10 showed the outstanding performance by achieving complete adsorption of all four SPx using only 80 μg of the adsorbent. The excellent adsorption efficiency of HP-UiO-66-NH 2 -10 was also obtained with a wide pH range and short adsorption time (10 min). Adsorption experiments demonstrated that the adsorption process involved chemical adsorption and multilayer adsorption. By utilizing X-ray photoelectron spectroscopy and density functional theory to explain the adsorption mechanism, it was found that various interactions (including coordination, hydrogen bonding, and electrostatic interactions) collectively contributed to the exceptional adsorption capability of HP-UiO-66-NH 2 -10. Those results indicated that the defect strategy not only increased the specific surface area and pore size, providing additional adsorption sites, but also reduced the adsorption energy between HP-UiO-66-NH 2 -10 and SPx. Moreover, HP-UiO-66-NH 2 -10 showed a low limit of detection (0.001−0.01 ng•mL −1 ), high precision (<13.77%), and accuracy (80.10−111.83%) in serum, liver, and cells, good stability, high selectivity (SPx/glucose, 1:100 molar ratio), and high adsorption capacity (292 mg•g −1 for SPx). The practical detection of SPx from human serum was also verified, prefiguring the great potentials of defective zirconium-based MOFs for the enrichment and detection of SPx in the biological medicine.