The 'Jinhua' pecan cultivar is valued for its nutritional richness and sweet flavor profile. However, post-harvest storage often triggers browning in 'Jinhua' pecan kernel pellicles, leading to quality deterioration. This study investigated changes in kernel pellicle color, associated enzyme activities, and total phenolic content (TPC), and their interrelations. The results revealed a highly significant correlation between polyphenol oxidase (PPO) activity, TPC, and the color change in the kernel pellicle. This indicates that PPO activity and TPC play crucial roles in browning of 'Jinhua' pecan kernel pellicle. Additional analyses included phenol detection and transcriptome profiling in the kernel pellicle post-harvest. Thirty major phenolic metabolites were identified, with 10 specific differentials implicated in kernel pellicle color browning. Transcriptome sequencing identified two crucial genes related to PPO synthesis, CiPPO1 and CiPPO2. Functional verification experiments confirmed that VIGS-silencing these genes significantly reduced leaf browning in pecan seedlings, indicating their pivotal role in promoting postharvest kernel pellicle browning. Furthermore, the findings provide new insights into the mechanisms of kernel pellicle browning and aid in the development of browning-resistant varieties.