<p><i>Taxillus chinensis</i> (DC.) Danser (<i>T. chinensis</i>) is a significant medicinal plant, with its seeds classified as recalcitrant and highly sensitive to chilling stress. Understanding <i>T. chinensis</i> seed response to chilling is crucial for developing effective long-term cryopreservation strategies. In this study, we investigated the viability, enzyme activities, phytohormone levels, ultrastructure, and proteomic profiles of <i>T. chinensis</i> seeds under chilling treatment. The results revealed that chilling stress significantly altered activities of antioxidant enzyme, including ascorbate peroxidase (APX), superoxide dismutase (SOD), and catalase (CAT). Phytohormone profiling demonstrated that the level of abscisic acid (ABA) increased rapidly under chilling stress, while the levels of indole-3-acetic acid (IAA), gibberellic acid (GA₃), and zeatin riboside (ZR) decreased. Transmission electron microscopy revealed ultrastructural damage, including organelle degradation, starch granule aggregation, and increased cellular vacuolation. Additionally, proteomic analysis demonstrated significant downregulation of differentially expressed proteins (DEPs) after 12&#xa0;h and 36&#xa0;h of chilling. Bioinformatics analysis suggested that these DEPs were associated with energy metabolism, signaling transduction, and photosynthesis, which compromised ribosomal protein synthesis. This study provides the first comprehensive molecular insights into the chilling sensitivity of recalcitrant <i>T. chinensis</i> seeds, enhancing our understandings of developing effective long-term conservation strategies for <i>T. chinensis</i> as a genetic resource.</p>