2-Methylisoborneol (2-MIB) is a volatile organic compound produced by a variety of actinomycetes, soil organisms and cyanobacteria, which is widely found in water bodies. To explore the effects of 2-MIB on fish, in this study, zebrafish were exposed to 42 ng/L 2-MIB for 24 hours. Comparative transcriptome analysis of gill tissues revealed that there were 163 genes up-regulated and 565 genes down-regulated significantly in the 2-MIB treatment group. KEGG pathway enrichment showed that oxidative phosphorylation related biochemical processes were up-regulated, while immune-related signaling pathways such as Toll-like receptor signaling pathway was down-regulated. RT-qPCR further showed that 2-MIB significantly up-regulated the expression of oxidative phosphorylation related genes, such as ndufb7, mt-cyb, mt-nd4, mt-nd6, mt-co2 and mt-atp6, while the immune-related genes rela, cd40, ikbkb, mapk8b, mapk3 and ripk1l were significantly down-regulated. Indeed, the activity of superoxide dismutase (SOD) increased in gills and liver after 2-MIB exposure. This study shows that 2-MIB can raise the level of oxidative phosphorylation in zebrafish and decrease the expression of genes related to Toll-like receptor signaling pathway.