[Background] Energy metabolism efficiency was an important component of measuring the utilization rate of the diet. Improving the digestion and metabolism efficiency of the energy contained in different nutrients by ruminants was helpful to improve the energy use efficiency of ruminants. [Objective] The objective of this study was to compare the structure and composition of ruminal microbiome of goats with different energy metabolism efficiency using Illumina MiSeq sequencing technology. [Methods] In total 19 goats were used as experimental animals, among them 5 goats with high energy metabolism efficiency were selected as HEU group and 5 goats with low energy metabolism efficiency as LEU group. Rumen fluid from each goat of HEU and LEU was collected and then total genomic DNA was extracted from the rumen fluids. High variable region of bacterial 16S rRNA genes was amplified by PCR using bacterial universal primers. Analyzing amplicon sequence data on the Illumina MiSeq sequencing platform and biological information analysis using QIIME software were done. [Results] Bacteroidetes (44.20%±9.39%), Firmicutes (16.40%±5.44%) and Proteobacteria (11.30%±7.42%) were the dominant bacteria in the rumen microorganisms of goats, among them Firmicutes was the dominant bacteria shared by the two groups. The relative abundance of Bacilli from LEU group (6.71%±2.47%) was significantly higher than that from HEU (P<0.05). The relative abundances of Lactobacillales of the two groups were the highest at the order level, and the relative abundance from LEU (4.98%±1.88%) was significantly higher than that from HEU (P<0.05). At the family level, the relative abundances of 7 families were significant differences in the two groups (P<0.05). The relative abundance of Bacteroidaceae was highest in the two groups, and Bacteroidaceae from group LEU (3.64%±1.32%) was significantly higher than that of group HEU (P<0.05). At the genus level, the relative abundances of 9 genus were significant differences (P<0.05). Only the relative abundance of Prevotella sp. from HEU (0.61%±0.36%) was higher than that in LEU (0.16%±0.07%), but the relative abundances of other 8 genus were significantly lower than LEU (P<0.05). The relative abundance of Ruminococcaceae sp. was the highest in HEU group (2.53%±0.62%) and LEU (4.19%±1.43%). [Conclusion] There are significant differences about structure and composition of rumen microorganisms among goats with different energy metabolism rate.