The pericarp browning and postharvest microbiological decay of litchi fruit (Litchi chinensis Sonn cv Kwai Mai) significantly reduce its commercial potential in the fresh market. In this study, different combinations of modified atmosphere packaging (MAP) were applied at 5 ± 1 °C based on the use of natural gases that are innocuous to human health and an alternative to commercially adopted sulfur dioxide (SO2) treatment. The results showed that control fruits, after 6 days of storage, begin to show the first symptoms of decay, revealed by the appearance of lesions and microbial infections determined by total mesophilic microorganisms and molds. This is not the case in the MAP-treated fruits and the MAP 3-treated (5% O2 + 20% CO2 + 75% N2) fruits that show the best results. The control fruits, moreover, turned completely brown by the end of the storage period. The MAP 3 treatment was the most effective in preventing browning and the loss of the red pericarp color and vitamin content and in maintaining acceptable SSC/TA levels and flavor. In addition, a microbiological analysis revealed that all the MAP-treated litchi fruits did not harbor undesirable microorganisms during the entire cold storage period. In conclusion, the MAP 3 conditions delayed pericarp browning and maintained the better organoleptic quality of litchi fruits.