Simple Summary: The development of the sheep industry plays an important role in increasing the income of farmers and herdsmen and promoting rural revitalization. Genetic improvement is the key to improving the competitiveness of the sheep industry. Tianhua mutton sheep, as China's first mutton fine wool sheep adapted to alpine pastures, have a key advantage over Gansu alpine fine wool sheep in terms of adaptive ability. In order to show the differences in rumen development and microbial structure between Tianhua mutton sheep and Gansu alpine fine wool sheep, the present study was conducted to comprehensively investigate the rumen of the two types of fine wool sheep by Hematoxylin Eosin (H&E) staining, volatile fatty acids (VFAs) assay, and full-length sequencing of 16S rRNA. The results showed that Tianhua mutton sheep had a better performance in the rumen volatile fatty acid content, rumen tissue development, and rumen microorganisms compared with Gansu alpine fine wool sheep, and this study provided a good theoretical explanation for the better adaptation of Tianhua mutton sheep to alpine pastures compared with Gansu alpine fine wool sheep. The purpose of this experiment was to investigate the differences in rumen tissue morphology, volatile fatty acid content, and rumen microflora between Tianhua mutton sheep and Gansu alpine fine wool sheep under the same grazing conditions. Twelve 30-day-old lambs were randomly selected from two different flocks in Duolong Village and grazed together for a period of 150 days. The rumen tissue was fixed with 4% paraformaldehyde and brought back to the laboratory for H&E staining, the volatile fatty acid content of the rumen contents was detected by gas chromatography, and the rumen flora structure was sequenced by full-length sequencing of the bacterial 16S rRNA gene using the PacBio sequencing platform. The acetic acid and total acid contents of the rumen contents of Tianhua mutton sheep were significantly higher than those of Gansu alpine fine wool sheep (p < 0.05). The rumen papillae height of Tianhua mutton sheep was significantly higher than that of Gansu alpine fine wool sheep (p < 0.05). The diversity and richness of the rumen flora of Tianhua mutton sheep were higher than those of Gansu alpine fine wool sheep, and Beta analysis showed that the microflora structure of the two fine wool sheep was significantly different. At the phylum level, Firmicutes and Bacteroidetes dominated the rumen flora of Tianhua mutton sheep and Gansu alpine fine wool sheep. At the genus level, the dominant strains were Christensenellaceae_R_7_group and Rikenellaceae_RC9_gut_group. LEfSe analysis showed that Prevotella was a highly abundant differential species in Tianhua mutton sheep and lachnospiraccac was a highly abundant differential species in Gansu alpine fine wool sheep. Finally, both the KEGG and COG databases showed that the enrichment of biometabolic pathways, such as replication and repair and translation, were significantly higher in Tianhua mutton sheep than in Gansu alpine fine wool sheep (p < 0.05). In general, there were some similarities between Tianhua mutton sheep and Gansu alpine fine wool sheep in the rumen tissue morphology, rumen fermentation ability, and rumen flora structure. However, Tianhua mutton sheep had a better performance in the rumen acetic acid content, rumen papillae height, and beneficial bacteria content. These differences may be one of the reasons why Tianhua mutton sheep are more suitable for growing in alpine pastoral areas than Gansu alpine fine wool sheep. [ABSTRACT FROM AUTHOR]