Miiuy croaker (Miichthys miiuy), as an economically important marine fish is affected by numerous bacterial diseases. Infection by bacterial pathogen Vibrio anguillarum causes high mortality and great economic loss in aquaculture. To understand the immune response of the miiuy croaker to V. anguillarum infection, we analyzed the transcriptomic profile of V. anguillarum-challenged M. miiuy, and two cDNA libraries, namely, the normal library (Ctrl) and V. anguillarum challenged library (Van) were constructed. Combined with the whole genome-guided assembly, total 47,971 unigenes were acquired. Moreover, 2482 significantly differentially expressed unigenes were identified based on the expression patterns. Immune-related differentially expressed genes (DEGs) that were significantly up- or down-regulated after V. anguillarum injection were identified via enrichment analysis using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. To further understand the expression profiles that underlie the response to V. anguillarum infection, we investigated the DEGs that are related to pattern-recognition receptors and cytokines. The expression patterns of relevant DEGs were validated by qRT-PCR. Additionally, the expression profiles of DEGs that are related to pattern-recognition receptors and cytokines were further measured in miiuy croaker macrophages. This study is the first to identify and characterize the transcriptome of miiuy croaker in response to V. anguillarum infection. The results expand the general understanding of the immune defense mechanisms of miiuy croaker and provide helpful information for counteracting V. anguillarum infection.