Background Rice ( Oryza sativa ) is one of the main crops in the world, and more than 3.9 billion people will consume rice by 2025. Sterility significantly affects rice production and leads to yield defects. The undeveloped anthers or abnormal pollen represent serious defects in rice male sterility. Therefore, understanding the mechanism of male sterility is an important task. Here, we investigated a rice sterile mutant according to its developmental morphology and transcriptional profiles. Results An untagged T-DNA insertional mutant showed defective pollen and abnormal anthers as compared with its semi-sterile mutant ( sstl ) progeny segregates. Transcriptomic analysis of sterile sstl - s revealed several biosynthesis pathways, such as downregulated cell wall, lipids, secondary metabolism, and starch synthesis. This downregulation is consistent with the morphological characterization of sstl - s anthers with irregular exine, absence of intine, no starch accumulation in pollen grains and no accumulated flavonoids in anthers. Moreover, defective microsporangia development led to abnormal anther locule and aborted microspores. The downregulated lipids, starch, and cell wall synthesis-related genes resulted in loss of fertility. Conclusions We illustrate the importance of microsporangia in the development of anthers and functional microspores. Abnormal development of pollen grains, pollen wall, anther locule, etc. result in severe yield reduction. Electronic supplementary material The online version of this article (10.1186/s40529-019-0260-3) contains supplementary material, which is available to authorized users.