Abstract: This study utilized Nanjing 9108 as the experimental material. Glucoseamine selenium and glucoseamine iodine were foliar-sprayed during the grain-filling stage, with foliar application of water serving as the control (CK). After ten days of treatment, the flag leaves of the rice plants were collected for transcriptome sequencing analysis. The results showed that 270 and 292 differentially expressed genes (DEGs) were obtained under glucoseamine selenium and glucoseamine iodine treatments, respectively, with 42 DEGs commonly detected in both treatments. According to gene ontology (GO) enrichment analysis, the DEGs in CK vs Se were mainly enriched in biological processes such as cellular components, molecular functions, transmembrane transport, membrane constituents, transition metal ion binding, and transmembrane transporter activity. In contrast, the DEGs in CK vs I were primarily enriched in physiological processes such as intrinsic components of membrane, membrane constituents, cell periphery, membrane part, plasma membrane, anion transmembrane transporter activity, and terpene synthase activity. The kyoto encyclopedia of genes and genomes (KEGG) functional enrichment results revealed that the DEGs in CK vs Se were mainly enriched in pathways such as nitrogen metabolism, metabolic pathways, and biosynthesis of secondary metabolites. Three nitrate reductase genes, Os08g0468100(OsNR1), Os02g0770800(OsNR2) and Os08g0468700(OsNR1.2), and one gene delaying leaf senescence, Os08g0140300(TDC1), were initially screened. Notably, Os08g0140300(TDC1) was associated with eight pathways and may be a key gene in response to exogenous selenium. The DEGs in CK vs I were only significantly enriched in the biosynthesis of phenylpropanoids, and six genes related to lignin synthesis were initially screened: Os08g0277200(OsCCR), Os01g0294700(OsPOD), Os03g0121200(prx33), Os05g0135500(prx71), Os06g0695500(prx90), and Os07g0677600(prx115). This study provides basic data for further exploring the response mechanisms of rice to exogenous selenium and iodine and offers theoretical support for subsequent improvements in selenium and iodine accumulation and transport in rice.