<p>A novel epitope-imprinted polymer with specific recognition of trace tumor marker matrix metalloproteinase-9 (MMP-9) was synthesized and successfully applied for the enrichment, separation, and detection of the human serum samples. Based on catalytic domain characteristics containing zinc ion binding sites of MMP-9, an MMP-9 C-terminal nonapeptide was selected as the antigenic determinant template, while zinc acrylate and choline chloride-methacrylic acid were chosen as functional monomers. After optimizing the preparation conditions through single factor and mixed orthogonal experiments, molecularly imprinted polymers (MIPs) with a maximum adsorption capacity of 3.59&#xa0;mg/g and an imprinting factor of 2.50 were obtained. MIPs showed good repeatability and reproducibility, and better selectivity for similar proteins than NIPs, with a 99.97% adsorption rate for 5&#xa0;µg/mL MMP-9, which coincided with the results from sodium dodecyl sulfate polyacrylamide gel electrophoresis. The recovery of human serum samples spiked with nonapeptide was 90.04%, with a relative standard deviation (RSD) of 2.3% (<i>n</i> = 5), and the recovery of human serum samples spiked with MMP-9 protein was 75.05%, with an RSD of 0.88% (<i>n</i> = 5). The developed method had a linear range of 1–10 ng/mL for MMP-9, with a detection limit of 0.41 ng/mL. The synthesized MIPs were convenient, cost-effective and consistent. The results showed that they had the potential to be used as novel adsorption and enrichment materials. Moreover, they could offer valuable references for the further preparation of highly specific MMP-9 adsorbents.</p>