Abstract 
Mechanical damage during express transportation is a major driver of postharvest quality deterioration in fresh produce. In this study, we integrated physiological and biochemical assays with microscopic observations and multi-omics approaches to comprehensively characterize the consequences of transportation-induced mechanical stress in Fuji apples. Structural analyses revealed that mechanical injury caused immediate disruption of cell wall architecture, including polysaccharide depolymerization and increased exposure of functional groups. Microscopic and FTIR analyses confirmed that mechanical stress caused cell wall collapse, polysaccharide network depolymerization, and increased exposure of functional groups. Biochemical assays further demonstrated that damage markedly accelerated cell wall disassembly, as reflected by a 140.91% increase in pectin solubilization and a 91.24% rise in cellulase activity, while also intensifying lipid peroxidation (52.71% increase in MDA content) and enzymatic browning (93.20% increase in PPO activity). Non-targeted metabolomics revealed extensive metabolic reprogramming, including the accumulation of stress-related phenolics, inhibition of tryptophan metabolism, and disruption of lipid-derived signaling pathways. Moreover, mechanical stress profoundly reshaped the apple fruit’s epiphytic microbiome, shifting the community structure from protective Bacillus-dominated populations to spoilage-associated Metchnikowia yeasts with strong pectinolytic capacity. By linking macroscopic phenotypes with molecular and microbial signatures, this work provides mechanistic insight into how postharvest mechanical impact accelerates deterioration in apples and offers a scientific foundation for developing targeted intervention strategies in transport-intensive supply chains.