Chromatin remodeling plays an essential role in plant reproductive development. Our previous studies demonstrated that CHR721, a SWI/SNF-family chromatin remodeler, is essential for reproductive development in rice, as evidenced by a chr721 mutant exhibiting unrepaired DNA lesions during late meiosis and subsequent cell cycle arrest, ultimately causing sterility. Here, we observed defective pollen exine, anther epidermis, tapetal degeneration, and aberrant nutrient metabolism in the chr721 mutant, particularly in lipid mobilization. Lipid species essential for anther development, including phosphatidylcholine (PC), lysophosphatidylcholine (LPC), and phosphatidylethanolamine (PE), exhibited reduced accumulation in the mutant compared to the WT. We established the central regulatory role of CHR721-mediated transcription during anther development. RNA-seq profiling of the mutant uncovered many differentially expressed genes (DEGs) at the late-meiotic, uninucleate, and binucleate stages, revealing progressive transcriptional perturbations. Functional enrichment analysis (GO and KEGG) revealed significant associations with lipid metabolism-related pathways and biological processes necessary for anther development, including tapetal development and regulation of programmed cell death (PCD). These transcriptional regulations were consistent with the morphological characterization and lipidomic analysis of the anthers in the WT and mutant. All these results and previous studies suggest that CHR721 regulates transcription by influencing the chromatin status and provide novel insight into the transcriptional function of CHR721 in anther development in rice.