<p>The Pacific oyster (<i>Crassostrea gigas</i>), a species of significant economic importance in global aquaculture, faces increasing challenges due to climate change and salinity fluctuations in coastal environments. This study aims to explore the breeding potential of low salinity tolerance traits and dissect their genetic basis, thereby improving environmental adaptability and expanding aquaculture zones. A total of 845 oysters from 36 full families were exposed to a low-salinity challenge (10 practical salinity units) for assessing phenotypic variation, estimating genetic parameters, and dissecting the genetic basis of low-salinity tolerance. The variation in survival rates among families (0–27.27%) highlighted substantial phenotypic plasticity of low-salinity tolerance. Heritability estimates for low-salinity tolerance traits ranged from 0.141 to 0.277, indicating low to moderate level genetic control of the trait. The low genetic and phenotypic correlations were observed between low-salinity tolerance and growth traits. Using a high-throughput and cost-effective genotyping approach by low-coverage whole genome sequencing with genotype imputation, we genotyped 297 samples with contrasted performance in low-salinity tolerance and detected 3,830,446 high-quality single nucleotide polymorphisms (SNPs) for genetic analysis. Genome-wide association studies (GWAS) uncovered the polygenic architecture of low-salinity tolerance and identified 16 SNPs associated with eight genes involved in oxidative metabolism, transmembrane transport, and immune defense. This study performed the first estimation of genetic parameters for low-salinity tolerance in <i>C. gigas</i> and identified genetic markers and associated genes for the trait, providing valuable information toward genetic improvement of low-salinity tolerance in the oyster using both traditional and genomic selection breeding strategies.</p>