Objective To investigate the effects of Oct4 and Cdx2 knockdown on the expression of genes involved in ICM (Inner Cell Mass) and TE (Trophoectoderm) differentiation in cattle, and to elucidate the roles of Oct4 and Cdx2 in the early development of bovine embryos. Methods Oct4 and Cdx2 genes were knocked down in bovine embryos by RNA interference. Real-time quantitative PCR and immunofluorescence staining were used to observe the effects of knockdown on early embryo development and gene expression. Results Specific siRNAs against Oct4 and Cdx2 inhibited Oct4 and Cdx2 expression, respectively, in bovine embryos. Oct4 knockdown had no effect on embryonic cleavage and eight-cell proportions, although the blastocyst proportion was significantly reduced; moreover, the mRNA levels of Cdx2, Sox2, and Nanog were significantly reduced (P < 0. 05). Cdx2 knockdown inhibited the expression of Oct4 mRNA (P < 0. 05). Conclusions Oct4 controls the differentiation of bovine embryos by regulating the mRNA expression levels of Cdx2, Sox2, and Nanog.