Abstract:A composite microbial system MEG with high efficient and stable degradation of cotton stalks was screened through the method of multigeneration selection. This microbial system was inoculated to the cotton stalks, and then stationarily treated for 7 days. Afterwards, biogas fermentation was conducted. Compared to the condition of non-pretreatment, the gas production increased by 25%. DGGE analysis showed that the diversity of bacterial community structure in the biogas fermentation system of cotton stalks was more abundant compared to the condition of non-pretreatment. At the same time, comparison in the effects of inocula obtained from 6 kinds of domestication methods on daily and cumulative of biogas production of cotton stalks was conducted. The results showed that the inocula domesticated from the mixture of 5 kinds of activated sludge from river bed mud, sewage ditch, industrial wastewater bed, pond bed, and lake bed could be acted as effective inocula for biogas fermentation of cotton stalks. The daily gas production and cumulative gas production were higher compared to the inocula domesticated from one kind of activated sludge.