Basic understanding of molecular features of ovaries and comparison of biological events in ovaries of different beef cattle breeds with indigenous potential has been indicated to improve beef production. The objective of the study was to explore the basic molecular features of Xiangxi cattle ovary and to identify the biological processes generating the differences between the ovaries of Xiangxi and Angus cattle. For this purpose, RNA-seq technology was used to analyze transcriptome data between the ovaries of Xiangxi and Angus cattle. A total of 64.87 Gb clean data were obtained that contained 6.10 Gb clean data of each sample. A total of 109 differentially expressed genes were obtained from comparison of transcriptome analysis between Xiangxi and Angus cattle. Among the 109 differentially expressed genes, 60 genes were upregulated in Angus, whereas 59 genes were upregulated in Xiangxi cattle. Gene ontology and Kyoto Encyclopedia of Genes and Genomes Pathway Analysis indicated that many of these genes encode the proteins involved in signal transduction and ovarian development. In this study, the mRNA expression of ASIP, IGLL1, FOSB and IL17RD in ovary of Angus cattle was found to be upregulated. While, the mRNA expression of GSTA3, TICAM1, CCDC6 and TSPAN18 was upregulated in Xiangxi cattle. These observations could provide basic information to improve understanding of fertilization, ovarian development and immune cell functions in the Xiangxi cattle and other closely related cattle breeds.