The growing demand for early and precise disease diagnosis has made biomarker detection a vital component of modern precision medicine. However, conventional detection methods often struggle with cost, scalability, and robustness in complex biological samples. Molecularly imprinted polymers (MIPs), synthetic biorecognition materials that mimic natural molecular recognition mechanisms, have emerged as a transformative solution and gained increasing attention from the scientific community. MIPs are created by forming specific recognition sites within the polymer matrix using target molecules as templates. These sites enable MIPs to recognize the target molecules with high sensitivity and specificity, making them highly promising for applications in biomarker detection. The aim of this review is to comprehensively summarize the latest research on the application of MIPs in clinical diagnostic biomarker assays from 2021 to 2025, with a particular focus on (1) composition and structure of MIPs; (2) preparation methods; and (3) the use of MIPs for biomarker detection. Through an in-depth analysis of these studies, this review endeavors to provide valuable insights and guidance for future medical research and clinical applications involving MIPs.