Aquaporin (AQP) is a transmembrane transport protein that plays an important role in biological processes such as water balance and osmotic pressure regulation. The blunt snout bream (Megalobrama amblycephala) is a unique herbivorous freshwater economic fish species in China that presents limited growth at a salinity of 2. To further investigate the structure and function of AQPs in the blunt snout bream and its adaptive characteristics under salinity stress, 19 AQP genes were identified throughout the entire genome of the blunt snout bream using bioinformatics methods, which showed that they were unevenly distributed on 12 different chromosomes. According to the phylogenetic relationships, gene structure, and motif analysis, the AQP of the blunt snout bream can be divided into four subfamilies. Moreover, the gene structure, motif composition, and sequence of the same subfamily were relatively similar. Multiple sequence alignment of the AQP protein sequences of the blunt head bream with other bony fish and higher vertebrates was performed, and a phylogenetic tree was constructed. The results revealed that the AQP of the blunt head bream was highly conserved during the evolutionary process, which is of great significance for further research on the role of the blunt head bream AQPs. The qRT PCR study showed that the expression of 19 AQPs was generally low in 10 tissues, including the gills, kidneys, intestines, and liver of the pufferfish. Among them, only the expression of AQP3b was highest in the gill tissue responsible for osmotic pressure regulation. AQP8a.2 was highly expressed in the intestine, while AQP12 was highly expressed in the liver tissue. Further research has shown that under salinity stress of 2–4, there is a positive correlation between the volume change of interlayer cell clusters (ILCM) in the gill tissue and the expression level of AQP3b in the gills of the blunt snout bream. In the initial stage of salt stress, the expression level of AQP3b gene significantly decreased with the increase of stress time (P＜0.05), but gradually recovered after adapting to salt stress.This indicates that the blunt snout bream undergoes gill remodeling under salinity stress to maintain osmotic pressure balance within the body. This research result indicates that AQP3b plays an important role in salinity adaptation and osmotic pressure regulation in the gill tissue of blunt snout bream. The systematic study and analysis on the AQPs of the blunt snout bream revealed that members of the family of AQPs exhibit evolutionary and functional conservation. The study on the morphology of the gill tissue and expression level of AQP3b in the gills of the blunt snout bream showed that tissue and gene coordination occurs in response to salinity stress and has positive regulatory effects on osmotic pressure changes, thereby helping the fish to adapt to environmental changes more quickly. The results of this study provide a molecular basis for further research on the adaptation mechanism of blunt snout bream.