Lignification is a typical symptom of chilling injury (CI) in loquat fruit under chilling stress. This study investigated the impact of hydrogen sulfide (H2S) on endogenous H2S, shikimate, phenylpropanoid, and cell wall metabolisms of loquat fruit during refrigeration. The findings suggested that H2S treatment hindered the rise in the CI index and firmness while delaying the reduction in extractable juice, soluble sugar, and titratable acid content of loquat fruit. Besides, H2S treatment promoted the endogenous H2S content, which was correlated with the increase in activities of related H2S synthase enzymes. Furthermore, H2S suppressed enzymes involved in shikimate and phenylpropanoid metabolisms, thereby decreasing phenylalanine and lignin accumulation. Simultaneously, H2S treatment retarded the increases in insoluble pectin, hemicellulose, and cellulose by orchestrating cell wall-modifying enzymes. This work indicates that H2S treatment may alleviate chilling-induced lignification by inhibiting lignin accumulation and enhancing the depolymerization and solubilization of cell wall polysaccharides.