Male sterility is defined as failing to produce functional pollen during stamen development in plants, and it plays a crucial role in plant reproductive research and hybrid seed production in utilization of crop heterosis. High throughput RNA sequencing (RNA-seq) has been used widely in the study of different fields of life science, as it readily detects all the mRNA and non-coding RNA in cells. Recently, RNA-seq has been reported to be applied in different species and kinds of pollen abortion types in plants, which has contributed to the understanding of the molecular mechanism and metabolic networks of male sterility at the transcription level. In this review, we summarize research progress on the mechanisms of male sterility in plants, focusing on RNA-seq analysis encompassing strategies of RNA library construction, differentially expressed genes and functional characteristics of noncoding RNAs involved in stamen abortion. Furthermore, we also discuss application of transcriptome sequencing technology to elucidate pollen abortion mechanisms and map fertility-related genes. We hope to provide references to the study of male sterility in plants.