In order to study the effects of intermittent aeration on greenhouse gas emissions and bacterial community succession during membrane-covered aerobic composting, a large-scale aerobic composting experiment was carried out. Two different aeration intervals designed to maintain the temperature of the compost was in 50–65 °C. The control group and experimental group were set to 10 min–10 min (on-off) and 10 min–30 min (on-off), respectively. The results indicated that the emissions of methane and nitrous oxide from the outside of the membrane in the control group were 9.68% and 47.10% less than those in the experimental group. And the global warming potential was 9.77% less than that in the experimental group. Wilcoxon rank-sum test result indicated that Tenericutes was a significantly different phylum between the two groups and played an important role in cellulose degradation. Redundancy analysis indicated that C/N had the greatest influence on the distribution of the bacterial community. It also found that Pseudogracilibacillus and Tepidimicrobium were significantly correlated with nitrous oxide and carbon dioxide emission rates, respectively. Therefore, adjusting aeration interval time during the membrane-covered aerobic composting could be a useful strategy for limiting greenhouse gas emissions and effecting bacterial community structure.