Fresh goji berries are prone to decay and spoilage, resulting in economic losses. We investigated the effects of carvacrol (CVR) on the natural disease incidence and quality of goji berries by fumigating with varying CVR concentrations (0.06, 0.12, and 0.24 μL/mL). The results showed that CVR treatment inhibited the natural decay of goji berries by enhancing their quality, color, and total soluble solids/titratable acidity ratio. Moreover, 0.12 μL/mL CVR was determined to be the optimal concentration, as it maintained the sensory quality (except for aroma) and inhibited the disease incidence and preliminary disease expansion of goji fruit inoculated with Alternaria alternata. The treated berries exhibited elevated total phenolic content, total flavonoid content, ascorbic acid, glutathione, melatonin, total chlorophyll, and carotenoid levels. Higher hydrophilic and lipophilic total antioxidant activities and free radical scavenging capacities were also observed in the treated berries. Targeted metabolomics showed that treatment with 0.12 μL/mL CVR increased the levels of four phenolic acids (caffeic acid, chlorogenic acid, ferulic acid, and protocatechuic acid) and two flavonoids (naringenin and quercetin) in goji berries, thereby activating the gene expression of the phenylpropanoid metabolic pathway. In summary, CVR treatment delayed fruit senescence and the decline in fruit quality, promoted the accumulation of bioactive compounds, and improved antioxidant capacity and disease resistance by activating the phenylpropanoid metabolic pathway.