Temperature is one of the environmental factors affecting the physiological activities of aquatic animals. This study explored the gene expression and regulation mechanism in the gill tissues of the scallop Mizuhopecten yessoensis under the stress of high temperature fluctuations. We designed a high temperature fluctuation experiment, in which the water temperature was raised from 20 C to 23 C and 26 C and then decreased from 26 C to 23 C and 20 C, with a rate of heating and cooling of 0.5 C/ h. The experiment consisted of four cycles and lasted for 7.5 days. When the target temperature was reached and the next temperature increase or decrease began, the gills of scallops were collected to measure immune enzyme activities and for transcriptome analysis. Immunological results showed significant differences in enzyme activities of catalase, superoxide dismutase, total antioxidant capacity, and lysozyme in scallop gills at 20 C on the first day and 26 C on the fifth day. Therefore, we analyzed gene expression from gill samples from these two time points using transcriptomics. We referred to samples from these time points as the normal temperature group (NT) and high temperature group (HT). Transcriptome results indicated that 347 differentially expressed genes (DEGs) were found in HT versus NT. Through gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found that these DEGs were mainly involved in metabolic pathways and protein synthesis pathways and had significant effects on oxidative stress, apoptosis, body metabolism, and protein folding in M. yessoensis. We selected 62 DEGs related to heat shock, immunity, and metabolism, including 47 upregulated and 15 downregulated DEGs. In a subset of these genes, quantitative real-time PCR (qRT-PCR) analysis showed similar expression (R 2 = 0.81), thus validating the transcriptome data. Our results provide a theoretical basis for further analysis of the response mechanism in M. yessoensis to high temperature stress and for the development of molecular breeding technology for high temperature tolerance.