The aim of this study was to explore the role of in stress-responsive regulation of roughskin sculpin () under low salinity stress. Firstly, sequences of these genes were obtained from transcriptome data of , and phylogenetic analysis was performed. In this study, fish were subjected to two different acute osmotic treatments (salinity changing rate at 27 and 1.1 ppt/h), expression patterns of the three genes in the four target tissues (gills, intestines, kidney, and liver) were examined using qRT-PCR. Phylogenetic analysis revealed that genes respectively formed an independent cluster, in which protein shared high identity with those of Perciformes, Cypriniformes, and Cyprinodontiformes species, teleost proteins formed a single lineage distinct from those of other vertebrates. Tissue-specific gene expression patterns in all three target genes showed that each tissue had a specific gene expression pattern in response to salinity changes. In the gills, the expression of increased significantly at 12 h, but different expression patterns were identified in the other tissues. In the intestines, the expression of decreased significantly at 48 h under the relative chronic salinity stress, while the expression of significantly increased; under the acute salinity stress, mRNA levels of increased significantly at 24 h, and the expression of HSPB1, HSPB7, and was significantly upregulated at 24 h in response to the relative chronic salinity stress; under the acute salinity stress, the expression of HSPB11 were significantly upregulated. The expression of HSPB1 expression was detected under chronic salinity stress, but a significantly upregulated expression was found under the acute low salinity stress; the expression of was significantly upregulated under both treatments. These results demonstrate the differences among expression profiling in the stress-responsive regulation activity of , these findings could provide a theoretical foundation for revealing the role of small heat shock proteins in fish stress-responsive regulation and the molecular mechanism of migratory fish salinity adaptation.