Background: Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, have a suite of adaptive features to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear.Results: This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing in order to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DEGs), 389 differentially expressed lncRNAs (DELs), and 73 differentially expressed miRNAs (DEMs) were identified between Tibetan (TC) and Chahua chickens (CH). Functional analysis revealed that several important DEMs and their target DELs and DEGs are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DEGs-DEMs-DELs interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions: These transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insight into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.