In order to investigate the variations of gene expression of Larimichthys crocea under high temperature stress, two libraries of high temperature treatment group and control group were constructed and sequenced using the Illumina HiSeq 2500 platform (paired-end). High temperature treatment group (heat1, heat2, heat3) and control group (control1, control2, control3) obtained 15.28 Gb and 13.92 Gb raw data respectively, and the average GC content of each library was 51%. After strict filtering, clean reads were then mapped to the Larimichthys crocea reference transcriptome using the Bowtie 2 software, the amount of gene expression were also estimated according to the reads mapped to genes. EdgeR software package was then used to determine the differential gene expression of 2 groups of samples with a threshold criteria FDR < 0.05 and |log2(FC)| > 2. Totally 1259 differentially expressed genes (DEGs) were identified under high temperature stress, among which 821 genes were up-regulated and 438 genes were down-regulated. Twelve DEGs were random selected for quantitative RT-PCR (qRT- PCR) analysis, and the results confirmed that the transcriptome analysis was reliable. Furthermore, the DEGs were subject to GO and KEGG enrichment analysis, the results showed that most of the DEGs were involved in oxidation-reduction, reduction reactions, protein folding and defolding, glucose and lipid metabolism, and the occurrence of certain diseases. The results above mentioned provide foundation information for further study on the molecular mechanism of high temperature tolerance in Larimichthys crocea.