The tiger grouper, Epinephelus fuscoguttatus, is an economically important fish in Southeast Asia but has been plagued by several diseases. Spatholobus suberectus (S), Phellodendron amurense (P), and Eclipta prostrate (E) are three commonly used Chinese medicinal herbs. Although previous pharmacological and clinical studies indicated that S, P, and E possess a variety of beneficial functions in mammals, little is known about their functions in farmed fish and the underlying molecular mechanism of their actions. Challenge tests in this study showed that after 14 days of diet supplement, all these herbs could effectively enhance the disease resistance of E. fuscoguttatus against Vibrio harveyi. However, the non-specific immune parameters of the herb-supplemented groups were not significantly different from the control group. To further explore the molecular mechanism of herbal immune-regulating effects on E. fuscoguttatus, transcriptome sequencing and RNA-Seq technique were applied on E. fuscoguttatus kidney. De novo transcriptome assembly of E. fuscoguttatus kidney yield 80,014 unigenes, among which, 44,901 (56.12%) were annotated with at least one of the public databases (Nr, Nt, Swiss-Prot, KEGG, COG, GO). Among these, 22,738, 11,700 and 27,457 unigenes were assigned to 57, 25 and 258 categories of GO, COG and KEGG databases, respectively. Using Solexa/Illumina's DGE platform, a total of 231, 186 and 144 putative differentially expressed genes (DEGs) were detected in P, E and S group compared with the control group. GO analysis indicated that in P and E, down-regulated DEGs were dominant in almost every GO term; whereas in S, up-regulated DEGs were more dominant. KEGG pathway analysis revealed that putative DEGs in all three herb groups were obviously enriched in the pathways related to infective diseases and immune system. We also identified a number of immune relative genes and pathways (TLR5, IL8 and MAPK pathway, for instance) associated with P, E and S's regulatory effects on E. fuscoguttatus. This study will enrich the E. fuscoguttatus transcriptome database, contribute to a better understanding of the molecular mechanisms associated with the immunoregulatory activities of Chinese medicinal herbs on teleost and provide valuable information on the prevention of grouper Vibrio diseases using Chinese medicinal herbs.