Fresh goji (Lycium barbarumL.) berries were treated with high-concentration (50% and 90%) oxygen shocking for 30 min and then stored at 0 ± 0.5 °C for 30 d. Decay, aerobic plate count, firmness, weight loss, total soluble solid (TSS), and titratable acidity (TA) were evaluated during storage. A total of 90% O2shocking more effectively reduced decay and maintained the weight loss and firmness of goji berries. Subsequently, changes in fungi communities were analyzed using high-throughput sequencing (HTS) in the 90% O2-shocking and control groups. The results showed that 90% O2shocking retained the richness and diversity of fungi communities and the microbiome was related to the quality properties of the fruit. Thus, we inferred that high oxygen shocking inhibited the development of natural decay and maintained the satisfying quality of goji berries by affecting the fungi community composition, which reduced the growth of pathogenic fungi and harmful saprotrophic fungi in the genera, such asFilobasidiumsp.,Alternariasp., andCladosporiumsp. We provide a new insight into the disease development and quality changes during the storage of postharvest goji berries.