Abstract: Gene sequencing was performed on the endophytes of 18 samples of the contral group(C) and the two groups(W, Y) of cinnamon leaves and twigs after biological pretreatment. The analysis of species composition found that the number of unique species in group C was 56, group W was 50, and group Y reached 100; the abundance of Proteobacteria in the three groups of samples was higher, and the total abundance accounted for 96%. A comparative analysis of 18 samples found that Y2 and W4 have significant differences. Species difference analysis and comparison of group C found that Firmicutes among the three groups were significantly different. The LEfSe multi-level discriminant analysis of species differences between the W and Y groups found that the abundance of Methylobacterium in the W group had the greatest impact on the difference; in the Y group, Firmicutes had the most significant difference between the groups. At the same time, its abundance has the greatest impact on the difference effect.