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The Chinese wolfberry branch, normally as agricultural wastes, is one of the most important renewable and reuseable resources of plant fibers in Ningxia. To improve the efficiency of wolfberry branch utilization, the characteristics of lignocellulose degradation, microbial community metabolism and diversity were studied during the fermentation of wolfberry branches substrate. By design of orthogonal experiment, wolfberry powder branches and sophora alopecuroides stem powder mixed in ratio of 4∶1 were used to study the influence of fermentative factors on microbial community structure and diversity during the fermentation by Biolog—ECO system. The results showed that at the end of the fermentation, the degradation rates of cellulose, hemicellulose and lignin were stayed above 15%, 19% and 10%, respectively. The treatment, which added oil cake and inoculated with coarse cellulose degrading bacteria, got the higher degradation rates of lignocellulose at temperature of 60℃, moisture content of 60%, and the degradation rates of cellulose, hemicellulose and lignin were 18.12%～19.22%, 23.55%～25.21% and 13.87%～14.24%, respectively, which were increased significantly than those of the other treatments;microbial activity and diversity during high temperature period were increased. Average well color development of microbes were 1.019, 1.062, 0.943 and 1.117, and Shannon—Wiener index, Simpson index and richness index of microbes were 2.321～2.365, 0.930～0.941 and 18.78～20.33, respectively. The ability to metabolize microorganism on part of carbon source was improved, which resulted in promoting degradation of organic matter.