Oysters face a complex and changeable environment in the intertidal zone. Heat stress is the main cause of their mass summer deaths. Several important genes are identified to be associated with heat response for oysters. However, regulation of these heat response genes in oysters remains largely unknown. In this study, 27 RNA-seq datasets are used to give a relatively comprehensive of long noncoding RNA (lncRNA) sets for C. gigas. Then, the differential expressed genes and lncRNAs are identified under heat stress. Among all the heat shock proteins (HSPs) and inhibitor of apoptosis proteins (IAPs) in the C. gigas genome, 25 heat shock proteins and 14 IAPs are differential expressed. The Gene Ontology analysis reveals that differential expressed genes (DEGs) are enriched in 6, 7, and 7 GO terms in cellular components, molecular function, and biological process, respectively. Within these terms, cellular response to stimulus is the most abundant term. Furthermore, the potential cis target of the differential expressed lncRNAs (DELs) are predicted to investigate their functions. Of the 394 DELs, there are 80 DELs being found to be corresponded to 113 protein-coding genes. Of them, eight HSPs are found to be regulated by their lncRNA regulators under heat stress. This work provides valuable resource of lncRNA and their regulatory roles under heat stress in C. gigas and gives new insights into adaptive evolution in marine mollusks.