Selenium (Se) is required for the normal growth and development of aquatic animals. However, excessive Se can have various toxic effects on aquatic animals. In this study, we performed transcriptome analysis to determine the mechanism by which immunity and growth of abalone are affected by toxic dietary concentrations of Se. Four experimental diets were administered to supplement organic Se at concentrations of 0.00 (Control), 0.15 (Se15), 0.30 (Se30), and 0.60 mg/kg (Se60) to provide 0.16 (insufficient), 0.32 (optimal), 0.44 (super nutritional), and 0.60 mg/kg (toxic) Se concentrations in the diet. After feeding for 100 days, the results of the Gene Ontology (GO) analysis showed that the enriched GO terms of differentially expressed genes (DEGs) in the Se15 and Se30 groups were mainly focused on the cellular components, whereas the GO terms enriched in the Se60 group were mainly related to the metabolism of nutrients and the activities of various enzymes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the Se30 group were mainly enriched in various disease pathways, whereas the DEGs of the Se60 treatment were associated with the metabolism of various nutrients. Further analysis of DEGs showed that toxic dietary concentrations of Se decreased the immunity of abalone by affecting the biosynthesis and metabolism pathways of various nutrients. Additionally, toxic dietary concentrations of Se retarded the growth of abalone by decreasing the expression of various genes associated with shell formation, including lustrin A, perlucin, perlustrin, dermatopontin, chitin synthase, and chitinase as well as the genes associated with muscle production, including collagen, myosin heavy chain, myosin essential light chain, and paramyosin. In conclusion, the mechanism of the decrease of immunity and growth of abalone by toxic dietary concentrations of Se has been preliminary revealed in this study.