Allium mongolicum Regel (A. mongolicum) is a healthy edible plant but highly perishable with a short shelf life of 1–2 d. Modified atmosphere packaging (MAP) could inhibit the postharvest senescence and decay of the vegetables. Thus, the aim of this study was to apply MAP with different gas permeabilities to the storage of A. mongolicum and evaluate its effects on maintaining microbial communities and the postharvest quality of A. mongolicum. The results showed that polypropylene/poly(butylene adipate-co-terephthalate) (PP/PBAT, abbreviated as PAT) MAP was suitable for the storage of A. mongolicum by establishing an optimal atmosphere of 0.5–0.6% O2 and 6.2–7.1% CO2 in the bag. It could delay the postharvest senescence of A. mongolicum and maintain its quality by slowing down its respiration rate and weight loss, reducing cell membrane permeability and lipid peroxidation, maintaining the cell wall, and reducing infection and the growth of microorganisms. However, A. mongolicum in HPT was more perishable than that in PAT during storage. Pseudomonas was found to be the main spoilage bacteria, and they could also be effectively inhibited by PAT-MAP. The next-generation sequencing results also showed the growth of Escherichia-Shigella, Clostridium sensu stricto 1, Streptococcus, Aureobasidium, Didymella, and Fusarium, responsible for A. mongolicum decay or human disease, was well inhibited by PAT-MAP. The results suggested that PAT-MAP could be used to maintain microbial diversity and the postharvest quality of A. mongolicum under cold storage conditions. It provided a feasible solution for the preservation, food quality, and safety control of A. mongolicum.