The mechanism of transcriptional regulation has been the focus of many studies in the post-genomic era. The development of sequencing-based technologies for chromatin profiling enables current researchers to experimentally measure chromatin properties. Moreover, many studies aim at annotating the state of the chromatin into broad categories based on observed chromatin features and/or DNA sequences, then associating the resultant distal regulatory regions with the correct target genes based on DNA sequences, and predicting the dependence of epigenetic features on genetic variation. Stem cell biology has many applications in the area of regenerative medicine and tumorigenesis. In this review, we summarize recent research progresses on the application of next-generation sequencing techniques in studying transcriptional regulation in embryonic stem cells. This review mainly focuses on four areas: (1) microarray or RNA-seq; (2) chromatin immunoprecipitation (ChIP); (3) Dnase I hypersensitive sites (DHSs); (4) high-throughput chromosome conformation capture (Hi-C). These technologies have been utilized in studying chromatin on three levels, i.e., gene expression, transcription factor binding and genome three-dimensional structure. We especially emphasize three master transcription factors of pluripotency: Oct4, Sox2 and Nanog. We aim to track the frontier of stem cell transcriptional regulation research and share important progresses in this field.