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The visually appealing pink Auricularia cornea (PAC) underwent noticeable discoloration when stored at 4 °C, adversely affecting their eye-catching colors, texture, and commercial value. The mechanisms underlying the quality losses during storage remained understudied. Here, data from 12 physiological indicators, 14 texture or color-related indicators, and transcriptome dynamics across 6 stages spanning 35 d were comprehensively evaluated. The results reveal a loss of key quality indicators, such as color, hardness, springiness, cohesiveness, chewiness, and resilience, etc. Enzyme activities associated with low-temperature stress exhibit fluctuating patterns. Quality remains acceptable when refrigerated for seven days. RNA sequencing revealed 1,106 to 1,974 differentially expressed genes (DEGs), based on 4-fold changes and validated via RT-qPCR. DEGs were enriched in processes including cell wall macromolecule catabolism, oxidation-reduction, and alcohol metabolism, along with KEGG pathways related to amino acid, galactose, and lipid metabolism. This study offers valuable insights into optimizing the postharvest preservation of PAC during refrigeration. [Display omitted] • Refrigerated storage alter the phenotype and physical properties of pink A. cornea. • Fading, yellowing and texture softening were the main post-harvest storage indicators. • DEGs and functions associated with cell wall alterations were identified. • Oxidation-reduction and alcohol metabolism processes drive physiological changes. • DEGs related to amino acid metabolism were significantly enriched. [ABSTRACT FROM AUTHOR]