Abstract: 【Objective】 The aim of this experiment was to obtain the yak ovarian transcriptom during estrus and pregnancy,to identify the differentially expressed transcripts（DETs） between them,to explore the biological functions of DETs,and to analyze the molecular mechanism of yak reproduction during estrus and pregnancy,so as to provide a basis for further analysis of yak reproductive performance.【Method】 Yaks were naturally grazed and observed in Haiyan County,Qinghai Province. Three were selected,which were estrus and pregnancy for transcription. Astalavista software was used to identify the types of AS events.TADIS pipeline was used to identify the APA.【Result】 There were 2,479 and 2,053 AS events in estrus and pregnancy. The 9, 189 genes and 8924 genes were identified as having APA during estrus and pregnancy. There were 3562 differentially expressed transcripts（DETs） of which 1693 were upregulated and 1869 were downregulated. GO analysis revealed that the DETs were centred on cell processes,single tissue processes and biological regulations. Reproduction,reproductive processes and rhythm were related to reproduction. KEGG analysis showed that DETs were involved in 203 pathways. The PI3K-Akt signalling pathway,endocytosis,spliceosome and oxidative phosphorylation were the most important pathways. MAPK signalling pathway,estrogen signalling pathway,progesterone-mediated oocyte maturation,cell cycle,oxytocin signalling pathway and oocyte meiosis were associated with reproduction.【Conclusion】 The transcriptome study of ovary tissue in estrus and pregnancy of yak by using third generation sequencing technology revealed the number of differentially expressed transcripts under different physiological status of ovary tissue in yak,obtained the function,classification and metabolic pathway of differentially expressed transcripts,which enriched the ovary transcriptome information of yak,and laid a foundation for the study of genes related to reproduction and molecular mechanisms in yak ovaries in estrus and pregnancy.